I know what you mean. I have done similar things and said to my self "I know he has xx but I need to make a move soon and am gonna do it any way" and sure enough he has xx. As well I was in a game last night and a guy 3 bet me on a wet flop after I had led out PF, I had KK and a BDSD, but an A J 9 and a FD showing I started thinking "na, hes bluffing, he is making a move here representing a number of hands that will dominate me, but his 3-bet will cost me so much that I have to shove over the top if I am gonna play and he has me covered. and I can survive with my still healthy stack if I fold, and he just might have it" and I folded and the clown showed his bluff. SO its hard to say. In both these cases my instincts were right, but upon dry reflection, I am not sure the decision I made was wrong either.
IMO this is one thing that will get easier with experience. I am at about 1500 games, maybe 1/2 those MTTs and the rest SnGs. I dont know how many hands, since I lost a majority of my HH due to a PC crash, and a lot of games are at PKR and they dont send you HH if you lose them. But I am starting to get a small amount of hands under my belt, and I still am not anywhere near experienced enough to think my decision making in these spot is as developed as much as I want it to be. I find myself thinking "bluff" when he has ze nutz and thinking "fold" when he has air more than I like.
So so get back to OP's question, I just try to listen to my instincts, and then try to figure out if the info I have coincides with my instincts. I am trying to prioritize my instincts under any info I may have.
But this may all change....