I think I've found a glitch.. and I'm really pissed about this one.
I'v collected all 40 Pokéathlon trophies; they were displayed in the Friendship room (the last room, with the gold statues) without a problem. Point is, to get the 10 Trust Trophies, you need 200 medalist pokémon, wich I had.
Then, I decided to get all my pokémon to be medallists, and started re-entering the courses and getting more medals. When I had about 260 medallist, I went to check the Friendship room again.. and it said I had only 32 trophies! 8 of my trust trophies were gone, even though the trust room still showed I had more than 200 medalist pokémon and collected all the trohpies.
Now I don't know if I get some more medals, the trophies will appear again, or what.
Edit: Yep, I can get more trophies, just need some more medallists.