I find that sometimes my companions abilities do not activate. This is usually with with ones that can trigger multiple times (and with flanking, but see my other post about that). I'm not talking about abilities that have a chance to trigger (repel boarders, burst fire, etc) but ones that should trigger all the time (first strike, vengeance, etc). I can't give much much info on when this happens, but it seems to happen on the enemies turn when my unit has triggered it during their turn.
Epic Talents can trigger multiple times during a fight (First Strike, Repel Boarders, etc.). It is my understanding that they can only trigger once per turn unless you have something like a level 2 or 3 ability. So, the first time it triggers during that turn will be the last time that turn that it will come into play. Next turn, it can of course trigger again if the conditions are met.
I was talking about the abilities that I have level 2 of. For example, my Ratbeard has first strike level 2. This means that I should get 3 first strikes in a round. But sometimes I don't have all 3 trigger even though the conditions are right. I see this happen most often (but not always) when I use one or two of the first strikes during my turn, and then in the enemies turn the left over ones to not activate.