The only one you don't get a second chance at is the Makuhita from the beginning and possibly the ones in the lab. A lot of them are in the Snagem Hideout post game, some are in Pyrite Cave, and the rest you just have to go back to talk to the guys who had them initially. And the boss pokemon can be second chanced in the Deep Colosseum in the post-game if you miss them both times.
Originally Posted by Shadow♠
In Fearful Day, In Raging Night, with strong hearts full, our souls ignite. When all seems lost in the War of Light look to the stars--For HOPE BURNS BRIGHT!
I don't care about my pokemon other than their battling potential. If they aren't good at battling, I'm not going to use them. If I have to spend time getting my pokemon to be perfect, so be it. I'll battle your pokemon that are "raised with love" anytime, and you know what? I'll probably win.