None of these are exotic. They are the ordinary mistakes that come from running payroll in a spreadsheet at the end of a long month.
1. Calculating tax on gross pay
Tax is charged on taxable income, not on gross. Pension and rent relief come off first. Apply the bands directly to gross and you will overtax everyone — quietly, every month.
The employee rarely notices. They just take home less than they should.
2. Treating a bonus like ordinary salary
A bonus, overtime, or a thirteenth-month payment is not the same as regular monthly pay. Some statutory contributions are charged on regular emoluments only, which means folding a bonus into the ordinary salary figure can overstate what you owe.
Record irregular pay separately. It takes one extra field and it stops you paying more than you have to.
3. Sending all PAYE to your own state
Covered in detail in our guide on state of residence, but it belongs on any list of common mistakes. PAYE follows the employee's home, not the company's address.
4. Not keeping the working
When a revenue service, an auditor or an employee asks how a figure was reached, "the spreadsheet said so" is not an answer. You need to be able to show the steps: gross, deductions, taxable income, which bands applied, the result.
If your process cannot reproduce a number from six months ago, you do not really have a payroll process — you have a series of one-off calculations.
5. Rewriting history
This one is subtle and it is the most damaging. When you find an error in an old month, the temptation is to fix the spreadsheet. Now last month's payslip and your current record disagree, and you cannot tell which is right.
Approved payroll should be read-only. Corrections belong in the current period with a note, not applied retroactively to a month that has already been filed and paid.
6. Missing deadlines you didn't know existed
PAYE remittance, pension remittance, VAT for registered businesses, annual filings. Beyond those sit obligations many small employers have never had explained to them — the housing fund, the employee compensation scheme, the industrial training levy, mandatory health insurance above a certain headcount.
Whether each one applies depends on your size and your sector. Not knowing is understandable. Finding out from a penalty notice is expensive.
The pattern behind all six
Every one of these is a process problem, not a maths problem. The arithmetic of PAYE is not hard. Keeping it consistent, reproducible and on time across twelve months and a dozen people is the hard part — and that is exactly what a spreadsheet is worst at.
You can test the arithmetic side yourself with our free calculator, which shows every step of the working under the Nigeria Tax Act 2025 — effective January 2026.