Hello Itachi47,
Do you happen, by any "chance" (or, here, lack of), to have reach the limit of PC Storage?
You're limited to 900 pokémons, the ones in your party count as well as if they were in your PC, so that makes 60 boxes (with few empty spots in the 60th, depending on how many are in your team)
Once that limit reached, you can't catch another Pokémon until you release some, so I guess the ones you'd have gotten from boss rewards are just lost
sorry i have not reached full box pc limit, i still have about 13 more box free.