Challenges of business process automation, and how to avoid them

The challenges of business process automation in a company with several departments are rarely about the software. Projects stall because no one owns the whole process, exceptions were never written down, systems disagree about the same data, approvals get skipped, the accounting connection comes last, people aren't trained and nobody watches after launch. Each has a known fix, and most fixes come before the build.

This guide is for operations directors, controllers and department heads at companies with approval chains, auditors and more than one entity. For the build itself, see our guide on how to automate business processes.

What are the main challenges of business process automation?

One process passes through many hands: an order starts in sales, moves through operations and ends in finance. Problems gather at the handoffs, and some take months to show.

A useful lens is the Green Book, the U.S. Government Accountability Office's standards for internal control. It is written for the federal government, and GAO says nonfederal entities may apply it as a framework too.

Challenge	What it looks like	How to prevent it	Who owns it
No single owner	Every department fixes its own step	One process owner, a step owner per department	A senior leader
Unwritten exceptions	A manual queue that grows after launch	List every exception from real cases first	The process owner
Data that doesn't agree	One vendor, three versions	One source of truth per field, checks and reconciliation	Each master record's owner
Skipped approvals	Payments without the required approval	Approval limits in the rules, every step logged	Finance, with internal audit
Late accounting connection	Entries post to the wrong account, entity or period	Design from the ledger back	The controller
No training	Side spreadsheets and workarounds	Training by role, on real cases	Each department head
Nobody watching	A step stops quietly for weeks	Alerts, reviews and change control	The process owner

Who owns a process that crosses departments?

Often, no one. Sales owns intake, operations owns fulfillment, finance owns billing and IT owns the tools. A decision that touches all four, such as an order with no purchase order number, bounces between them while the project waits.

The Green Book is clear: people in key roles can assign responsibility to roles below them, "but they retain ownership for fulfilling the overall responsibilities assigned to them." So:

• Name one process owner for the whole result, such as the controller for supplier invoices.
• Name a step owner in each department to test their part.
• Write down who decides. Rule changes, approval limits and exceptions go to the process owner.

What about the exceptions nobody wrote down?

The procedure document covers the normal case. The people who do the work carry the rest in their heads: the customer who pays in two parts, the vendor who invoices one entity for goods delivered to another. Skip them and they land in a manual queue that grows every month.

The Green Book says documentation helps "retain organizational knowledge," so it doesn't sit with a few people. Before you build:

1. Pull three months of real cases, not a demo set.
2. List every exception and who handles it today.
3. Decide each one: a rule, a handoff to a named person, or a stop.
4. Track the exception rate after launch. If it climbs, a rule is missing.

What if your systems disagree about the same data?

Larger companies keep the same facts in several places: a customer in the sales and accounting systems, a vendor set up separately in each entity, one item under three codes. When the automation moves a record between systems, every disagreement becomes a failed step or, worse, a wrong one.

The Green Book describes quality information as "appropriate, current, complete, accurate, accessible, verifiable, retained as appropriate, and provided on a timely basis." To get there:

• Pick one source of truth for each field, such as a vendor's bank details.
• Use one reference per record. The Green Book names unique invoice and purchase order numbers as a guard against duplicates.
• Check data before it moves, and reject or flag entries that fail.
• Reconcile on a schedule: compare both sets of records and explain the differences.

How do approvals and controls get skipped?

Rarely on purpose. The automation runs under one administrator login that can do everything. The approval limits in the policy never reach the rules. A bypass added to clear a backlog is still there months later.

The Green Book says transactions are "authorized and executed only by persons acting within the scope of their authority." Segregation of duties means no one person "controls all key aspects of a transaction or event," and that extends to who designs, tests and switches on a new system. So:

• Write the approval matrix into the rules: limits by entity, department and amount.
• Give the automation its own account with only the access it needs.
• Keep an audit trail, in NIST's terms a record in time order that rebuilds the events from start to final result.
• Allow no bypass without a recorded approval and an end date.

Why should the accounting connection come first, not last?

Because the process ends there. Teams often build intake and approvals first and connect the accounting or enterprise resource planning (ERP) system in the last weeks. Then come the questions: which account, entity and location code, what happens in a closed period, how tax and currency work. Each answer changes the steps before it.

The Green Book's controls over recording cover a transaction's whole life, "from its initiation and authorization through its final classification in summary records." So:

• Start from the entry. Agree what the finished bill or journal entry looks like in the ledger, then design backwards.
• Bring the controller in during week one, not at testing.
• Post test entries early in a test copy of the ledger: a split across two entities, a credit note, a closed period.
• Avoid a go-live in close week.

Our guide to back office automation covers what finance keeps in its own hands.

Why do people work around a new process?

Because nobody showed them how it works or why. Approvers click yes without opening the details. A team keeps its old spreadsheet "just in case." New hires never learn it at all.

The Green Book counts training as part of competence and says to "tailor training based on the needs of the role." For an automation:

• Train by role: approvers, exception handlers and the process owner need different things.
• Use real cases, including a rejected item.
• Write a one-page guide for each role and add it to onboarding.
• Watch for side spreadsheets: each one marks a missing step or lesson.

Who watches the automation after launch?

If the answer is "the person who built it, when they have time," expect a quiet failure: a login expires or a connected tool renames a field, and a step stops, unnoticed, until a supplier asks about a late payment.

The Green Book says ongoing monitoring "is built into the entity's operations, performed continually, and responsive to change," and that system changes are "authorized, documented, tested, and independently reviewed." NIST's term for controlling those changes is configuration control. Before launch, set up:

1. Alerts on failures and on silence, so a run that didn't happen is noticed that day.
2. A weekly exception report to the process owner.
3. A monthly review of volumes, failures and approval times.
4. Change control: every rule or tool update is tested first.

What are the disadvantages of business process automation?

Automation pays off on the right process, but it is never free or finished:

• Upkeep costs money. Hosting, monitoring, updates and review time last as long as the process runs.
• Steps break when a connected tool changes. Software makers update their official connections (APIs) and retire old versions, so each change needs a test.
• A broken process gets faster, not better. The Green Book notes that automated controls "tend to be more reliable because they are less susceptible to human error." The same consistency cuts both ways: a wrong rule hits every item.
• Knowledge can sit with the builder. Ask for documentation, admin access and a handover plan in writing.

None of this rules automation out; it argues for a first process that is frequent, rule-based and settled. Our business process automation examples show twelve workflows that often fit.

How does Raileon handle these challenges?

With automation consulting, we map how work really moves: where it comes in, who touches it, which systems it passes through and where it waits. Then we rank what to automate first by hours and risk.

The same team builds and runs it. In our business process automation, rules run on their own, judgment gets a draft and a person approves anything that reaches a customer or moves money. Every action is logged, and when something fails, your Raileon team fixes it.

It starts with a free 20-minute call with the founder, then a written proposal: what each automation does, what needs approval and what it costs. Builds are priced by scope. Monthly care starts from $1,999 a month and covers monitoring, fixes, updates and a monthly review. Cancel any time. Your plan runs to the end of the month you've paid for. No exit fee.

FAQ

What are the challenges of business process automation?

The usual ones are no single process owner, unwritten exceptions, systems that disagree about the same data, skipped approvals, a late accounting connection, untrained staff and nobody watching after launch. Most are organizational, not technical, so they are fixed before the build starts.

What are the disadvantages of business process automation?

It costs money to keep running, its steps can break when a connected tool changes, and it repeats a broken process faster. Budget for upkeep, test after every change and fix the process before you automate it.

What problems can business process automation solve?

It removes retyping the same data into several systems, approvals waiting in someone's inbox, missed handoffs between departments and reports rebuilt by hand each week. It works best on frequent, rule-based work where a miss costs money or a customer.

Should we fix a process before we automate it?

Yes, if the manual version is unclear or departments disagree on how it should run, because automation repeats whatever it is given. Map it with the people who do the work, agree on the rules and exceptions, then build.

Planning an automation across departments?

Bring the process that crosses the most desks. On a free 20-minute call, we'll tell you which challenge you're likely to hit first and how to avoid it.

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