From the Leage 2 FAQ:

• Monsters only provide clue tokens if they become trophies, so the Warlock and Endless monsters do not provide extra clue tokens. These clue tokens are received upon defeating the monster, the trophies are not traded in for clue tokens.

If I have an encounter that lets me draw a monster from the cup and keep it as a trophy (such as finding a dead body encounter), do i get the clue tokens for it?

"upon defeating" so did you defeat the monster? no

It's not like it mattered. We totally dominated the game last night, with 16 clue token to spare (19 if I could have gotten the three from the Hound of Tindalos). We could never win the first scenario, but being able to win by sealing gates made a huge difference. Even Amanda Sharpe was rolling in clue tokens (she had 9 when she went through her gate, and she started with +1 Fight and +1 Sneak. It was awesome). Karma was making up for how many bad hands it dealt us for the first scenario. I believe we won this in an 8 investigator game in about 1-1/2 hours.

we finished with 15 clue tokens or something, I think it is too easy giving you tokens for toughness.

Yeah, but at least we had clues this time around. i keep thinking back to the first scenario, where Harvey defeated 10 monsters from a monster surge with a Flute of the Outer Gods. That would have been something like 20 clue tokens, in one shot!