I have all of the boss trophies except for Tabuu and the Ridleys now...I've had my share of difficulties getting each and every boss.
-Galleom once attacked a Bob-Omb when I HAD THE TROPHY STAND IN MY HAND...he died.
-Duon knocked the Trophy stand off more than once
-I kept getting the Trophy Stand too early in the battle with Tabuu...then one time, after I killed him, the screen was fading out and a Trophy Stand appeared...
-Meta Ridley's trophy fell into the abyss
-Porky, OH MY GOD...he took forever for me to get. I wanted to see his trophy in particular, to read the description and figure out about him (I'm interested in Earthbound...dangit Nintendo, give it to us on VC so I can play it already!) and...well, you've got a pretty long level there, and space on both sides of the boss fight. The...second try, I got the trophy. Then, I stupidly forgot that you can't just exit the level right then and there to save the trophy, and quit and lost it. After that, it took me about 20 tries (no joke) to get a Trophy Stand at the right time. I'm pretty sure the same thing that happened with Galleom happened here as well...attacking a bomb of some sort when he had a sliver of HP left.
As for enemies in general, I haven't tried them yet, really. I've gotten a couple on my tries for Boss trophies, some on my tries for 100% on some levels, but I haven't gone specifically for them yet. Starting tomorrow, that'll probably change. Though it's going to be annoying to do. Actually, I may just wait until I do the SSE over again; I want to do the whole thing on Intense, and I'll start a save file just for that. Intense will probably get me a lot of Trophy Stands, so it would probably make the most sense to just wait until I start that file, which I probably won't do until I get 100% on my first SSE file.