since she had family coverage from 1/1-11/30 on your TurboTax 8889 you must indicate you had family coverage for every month from January through November. I am assuming you had no disqualifying coverage that covered her after July.
I'm almost certain the reason you are having this issue is that you indicated on your 8889 that you only had family coverage through July.
The rules do say if one spouse has family coverage, both spouses are treated as having family coverage. However, if you were covered by a non-HDHP after July, the HSA limitation for you is 7/12 of 8550. Her family coverage is irrelevant in this case. So if you were not covered by a non-HDHP after July, you must check family coverage for Aug - Nov on your 8889
