If you are just paying the discrepancy and NOT recovering any amounts from the employee, then you'll do a general journal entry.  The debits will be some combination of EI expense (if the discrepancy was extra EI you had to pay), CPP expense (if the discrepancy was extra CPP you had to pay), and non-deductible interest and bank charges expense (if there was interest and/or penalties added to the amount owing.)

If you don't have an account for non-deductible interest and bank charges expense, just use your normal interest and bank charges expense account but make a note for your year-end accountant, as they'll need to know about this amount when they prepare tax returns for your business.

If you are recovering amounts from the employee, then the answer gets much more complex.

Just a reminder to always complete any PIER questionnaires from Canada Revenue Agency - just because they flag something as a possible discrepancy doesn't mean it's an actual discrepancy, and filling in the PIER can reduce or eliminate the amounts you end up having to pay.