As a generality, don't worry about it, suck it up when it happens and pray it is a smaller stack that has you oversetted
Set over set does happen but it is rare...
There is only two betting patterns that tips me of my tripped up twos are no good, I lead, original preflop raiser reraiser, some body after him moves in on a K92 flop. If either of these guys are bozos I'm going broke here, if neither of them are yahoos I assume that I'm up against AK AA KK and 99 from the later guy. Often times though I will be pot commited to seeing the hand out unless they are both really deep. If one of them or both is a known nutpeddler (more applicable to Stars than anywhere else) letting it go is even easier.
LP player makes it 3x to go, you call in the BB with 77. Flop is QQT it checks around turn is a 7 there is some activity and you are called in two spots with LP raising, river is K, and two people move in before you, or after you lead for 1/3 pot. This is a tough and very marginal fold/call situation, but I have folded bottom set correctly here more than incorrectly. It is a real situational situation to lay down the baby boat that comes down to whether you think he has KK misplayed, AQ KQ TT. Not saying let this one go everytime, but use your best judgement in the situation, having the table covered makes these choices easier.
Folding bottom set isn't something to make a habit of doing, just take your lumps like the rest of us when you are beat
Pretty much all the people I play against I will go broke or drag the pot with set over set. It doesn't concern me when I lose other than the grumbling about misfortune to catch a good enough hand to play for all the money and come up short.