Most payroll problems are not exotic. They are the same handful of avoidable mistakes, repeated. Knowing them is half the fix.
1. Using outdated contribution and tax tables
Contribution rates and withholding tables change. Last year's numbers quietly produce this year's errors. Confirm the current figures with each agency, and keep them current in whatever computes your payroll.
2. Computing in the wrong order
Applying withholding tax before statutory deductions inflates the tax. Deduct the employee share of SSS, PhilHealth, and Pag-IBIG first, then compute tax on the correct taxable base.
3. Mixing gross pay into 13th month pay
13th month pay is based on basic salary earned, not gross. Including overtime, allowances, and premiums overstates it. See how to compute it correctly.
4. Getting premium pay wrong
Holiday, rest-day, overtime, and night-differential rates stack, and the combinations are where errors hide. Drive premiums from actual attendance, not estimates. See the premium pay guide.
5. Missing remittance and filing deadlines
Late remittances trigger penalties and interest even when the amounts were right. Keep a consolidated calendar of every agency's schedule.
6. Making unauthorized deductions
Deducting loans, shortages, or property costs without a lawful basis or written consent is a common violation. Document authorization before deducting anything beyond statutory items.
7. Keeping messy, unreconciled records
If monthly runs do not reconcile with year-end reports, filing season becomes a nightmare and audits get risky. Keep payslips, timekeeping, and remittance proofs consistent all year.
Prevent them by design
Notice a theme: most of these come from manual work and scattered data. A payroll system that keeps tables current, applies them in the right order, ties pay to attendance, and preserves a clean trail removes most of these errors before they happen. That is exactly what BeavHR is built to do. Book a demo to see it against your own payroll.
Related reading
- The Complete Guide to Philippine Payroll Compliance
- How to Compute 13th Month Pay in the Philippines
- Holiday Pay, Overtime & Night Differential
Disclaimer: This article is general information, not legal or tax advice, and Philippine rules and rates change over time. Always confirm the current requirements with the relevant government agencies, DOLE, BIR, SSS, PhilHealth, Pag-IBIG, and the National Privacy Commission, or your legal counsel before acting. Last reviewed: July 2026.