Dillema, need information about thickening of the uterus

Patient: My girlfriend visited her gynacologist today and he noticed some thickening of the uterus. She is a couple days late which is a normal occurance for her and we always used condoms and were careful. Despite that he assume pregnancy and told her to make a test, we freaked out because it is unlikely to conceive while using condoms, which we did. Now we’re scared and don’t know if there could be some other explanations to this thickening? By all calculations she should have her period this week, could this be the reason for it?