It could very well be a mod that has nothing to do with pet relations (btw, my mod does not even change pet relations), like any mod changing pregnancies, pregnancy success chances, a playable pets mod or whatever pet or woohoo related mod. If you had a cat and a dog breed together, this is a 100% indication that you have a mod prevailing over mine.
Mine does prevent the interaction between cats and dogs.
It also does prevent pregnancies of pets that aren't able to reproduce. You might (theoretically) see two male dogs make out (if you have a mod that allows it on purpose or by accident or if such a bug shoud indeed exist), but if you don't have a conflicting mod installed, my mod would always prevent a pregnancy as a result of such an encounter as well as it would prevent cats of making out with dogs and vice versa.
Also, I can assure you that in my game at least, there never ever has been a bug with male pet pregnancies.