Well, I don't consider me having a tough time with the bosses being stuck in a Temple because I am already done with the Temple, just having a hard time beating the boss (i.e. The Parasite in Jabu Jabu's belly, and Ganondorf's Phantom)
But, The first time I played through Ocarina of Time I got stuck in The Water Temple, of course.
It was pretty easy, but I could not find a key, which was underneath the Sqaure that rises when the water is up inside that pillar thingy. I was really irritated because I really had no idea how to get that key, I cried a bit in the inside when I got the key. I was very happy.