Hello Community Users, We just wanted to add on to this thread with some tips to resolve this issue with pension thresholds that resolved the issue for the customer who posted here originally.

Try excluding and re-including employee.
Re-save all contribution plans to apply the correct threshold.
Run test pay run and calculations and see if they are correct on next pay run.
Then  re-save pension settings and it should allow you to not account for thresholds correctly.
You have the options to make adjustments on next month's pay run for already submitted incorrect figures

Any questions at all or if your situation differs please feel free to reply here, we'd be happy to help you.