The TIME MACHINE calculates the taxes for the current year in full, and then credits you with the amount of taxes you told it was already paid in the screen right before launching it. You're telling me she's still paying $1000/month in taxes deducted from her pay, and you expect she'll get a ~$6000 tax refund when she files taxes next year. So there's a bit of cash problem and you need to withdraw more from your investments.
The TIME MACHINE has mostly a resolution of one year and it must close the books on taxes each December 31. It would give her the tax refund on that date and that will reduce the amount that needs to be withdrawn to meet your expenses.
Your work-around of adding an Expense is fine. You can also add a one-time Income, not taxable, to recoup the expense on the date you expect the tax refund in 2026.
The amount deducted at source from her employer seems high. It indicates the employer is not aware of deductions she may have. You might want to consider filing this form with the CRA to reduce tax deductions at source:
https://www.canada.ca/en/revenue-agency/services/forms-publications/forms/t1213.html
If you do, it has to be done every year.
Also consider that EI and CPP contributions stop once you've paid up the maximum contribution amounts, so that it's common for high earners to get a boost in take-home pay later on in the year. On her last pay-slip check how much EI and CPP she's paid already. For 2025 the EI max is $1077.48 and the CPP max is $4,034.10 (plus a bit more for CCP2)