Box 16/17 on the T4 is the employee's CPP/QPP contributions.
Box 16A/17A is the employee's second CPP/QPP contribution.
This is not a software issue, because if you have a second contribution (box 16A/17A), you should logically have a first contribution (box 16/17). Technically, both amounts should be on the same T4.
If the last version of your T4 on your CRA My Account is not with box 16/17 and box 16A/17, On the same slip, we suggest you contact the CRA to see if you can combine both T4s to have only 1 but with the full amount reflecting your 2024 year.
Here is the link to contact the CRA.
https://www.canada.ca/en/revenue-agency/corporate/contact-information.html
OR
The temporary workaround:
Take the amount in 16A/17A and move it to 16/17.
Your feedback is valuable, and we will pass this to our development team.
