CRA payroll audit red flags rarely show up as one dramatic mistake. More often, it’s a handful of small payroll habits that don’t quite line up, and over time they start to look like a pattern. If you’re an owner, controller, HR manager, or operations lead, the stress usually isn’t the audit letter itself. It’s the scramble that follows: pulling timesheets, explaining contractor relationships, rebuilding taxable benefit calculations, and trying to make your payroll reports match what went to CRA.