For many small businesses, payroll lives in the background until something goes wrong. A frustrated employee questions their paycheck, or a notice arrives about a missed deposit. None of this is fun, and most of it is preventable.
You do not need to master every nuance of payroll law to reduce risk. You do need to know where problems commonly arise.
One of the biggest payroll trouble spots is overtime. Not everyone who is paid a salary is automatically exempt from overtime rules. Exemption generally depends on both the type of work and a salary threshold, which can vary by jurisdiction.
Misclassifying someone as exempt when they actually should receive overtime can lead to back pay claims, penalties, and strained relationships. Periodically review your salaried roles, especially borderline ones, to confirm they still meet exemption criteria.
Tax rates for withholding, Social Security wage limits, and state unemployment often change from year to year. If you are running payroll manually or with older desktop software, it is easy to miss an update.
Make sure your payroll system is applying current year rates. If you rely on a service provider, confirm that updates are automatic and that any new states or localities you operate in are configured correctly.
Even when the amounts are correct, timing mistakes can cause penalties. Late federal payroll tax deposits or late filings of quarterly returns like Form 941 can trigger automatic notices.
Set calendar reminders, use the scheduling tools built into your payroll platform, or delegate this tracking to your bookkeeper or CPA. The goal is to move away from relying on memory alone. When schedules change because your payroll size grows, update your reminders promptly.
Employees have a right to understand how their pay was calculated. Vague or incomplete pay stubs can undermine trust. In some jurisdictions, certain information is legally required on each stub.
Check that your pay statements clearly show hours worked, rates, gross pay, each type of tax or deduction, and net pay. If you use special codes, explain them somewhere accessible so employees are not left guessing.
Most payroll systems allow manual adjustments for things like bonuses, corrections, or one off deductions. If those entries are not reviewed carefully, errors can slip in unnoticed.
Consider having one person prepare adjustments and another person review them before each payroll is finalized. For very small teams, this might mean the owner quickly scanning a summary report before approvals go out.
Finally, many payroll problems drag on because nobody wants to admit confusion. It is common to see a situation where staff have been "making it work" with spreadsheets and manual tweaks long after the business outgrew that setup.
If payroll feels fragile or overly complicated, that is a signal, not a personal failing. Bringing in a specialist, even briefly, to review your configuration and suggest adjustments can pay for itself in reduced errors and peace of mind.
Payroll will always require some care. But if you steer around these common trouble spots, it does not have to be a constant source of anxiety for you or your team. For a comprehensive review, see our payroll compliance checklist and guide on multi-state payroll.
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