I've been going Brother x Sister/Cousin for a while a now and can't seem to get the inbred trait.
Brother/Sister marraiges are only allowed in certain religions, and those religions (in order to be playable that way without the inbred trait becoming epidemic after a dozen generations) have a bonus that you are five times less likely to get. The inbred trait. Also it happens more often the more successive generations you do it. At a certain point in a Zoroastrian game even with the 5* reduced chance, inbred starts popping up all over the place, and once it starts, anyone who manages to reproduce with that trait is very likely to pass it on (even more so I think if they marry a close relative themselves). So it happens, but only aged a while, but once it does it snowballs out of control.