Well that's the good part of hitting a set, it's very disguised for you (or your opponents) to notice it.
But here it comes down to your reads on the opponent to be able to make a fold. Does he limp with big hands like AA/KK/QQ? Probably no in most cases.
If you sit on for example AQ and flop comes AQ6 rainbow, you raised preflop, cbet on flop and he check raises you, you have to start thinking what hands that can be in his range.
If he continues this aggression it's of even more importance that you really try to see what hands he would play this way. Since you, in my example, has A and Q blocker, hands such as QQ or AA is not very likely. If the board texture doesn't change, the only hands he would barrel 3 streets with is either 66 or a pure bluff (with no draws out on the board)
I hope you understood what I wrote, but yes, it's hard to spot - that's the beauty of flopping sets.