I have a return that is linked to a spouse. The spouses income is entered on the schedule 2 and the box stating that her income is not zero had been ticked off however, the tax program still picked up the federal spouse or common-law amount on line 303. When we tired to e-file it wouldn’t let us because of this amount being incorrect however, we never did receive an error message with regards to this prior to trying to e-file. I un-linked the spouse and the program seemed to fix the problem. I just wanted to point out that there is some kind of linking issue with the program when not preparing both returns.
I have never had an issue like you describe and have been using Taxcycle since it’s initial year. I would suggest your issue is isolated and you should call support for assistance.