I've only had that sort of issue once and the family tree was huge. And the two sims in question were very distantly related. Like they were cousins but like third or fourth cousins. Plus it wasn't the active house hold I was playing so I just let it go. And I haven't had the problem happen since that one time and that was like two computers ago. So I do agree with the other simmers in that with the large family tree its probably not seeing them as being related anymore.