Keeping a close eye on your payroll calculations is a great way to ensure you have all the proper calculations you need for your own remittances as well as your employees' T4 forms. I can help explain what's going on.
Since you're running payroll for last year in the new year, the program wants to default to the new 2020 tax tables, even though your end date for that pay period is the end of 2019. The key thing to pay attention to here is the Cheque Date, since that's one of the things the program uses to determine which tables to pull.
In this case, you can change the Cheque Date on the Enter Payroll Information window as it should still allow you to access the 2019 tax tables for your employees. If not, it'll be a matter of manually making the necessary adjustments to the tax calculations on each pay cheque. Something like the CRA's Payroll Deductions Online Calculator may be able to help. Otherwise, I recommend speaking with a payroll tax professional for more assistance on this.
The other thing to pay attention to is your payroll item set up. Items can be set up in two ways: to have the earnings allocated for the pay period in which they're earned or to have the earnings allocated for the pay period in which they're paid. You can check your payroll items by selecting Lists from the top menu, choosing Payroll Item List, then double-clicking the item you'd like to review or edit.
I hope that helps! Give me a shout if you have more questions.