I've run into the same issue. It's a bug between S3, Principal residence detail form, T2091/T1255 forms where the software isn't picking up correct information or is calculating a capital gain/loss from details on the PR form. Will need to wait until S3 (and all corresponding forms) are approved for e-filing and updated a in future software release.

It's beyond frustrating to not be able to finish off otherwise simple returns, simply because they sold their principal residence.