Did you open the gate in the base? The one that requires you to wear something that boosts your SEXY stat? They all show up there after you defeated them properly once, meaning after you got the "[Character X] will now show up in the base now" message during battle. If you got the "End Battle" option, that means you've done everything correct, the only exception is Agitated Guy (the white lizard dude), who you still have to defeat normally after you got the message, and Skunky Hunk, who's in the bar in Shiptown (you need to open the gate of the base on Pine Island before you can talk to him). After that, they all show up in the base, even though they keep appearing on the map as enemies. This is simply so you can still farm them for stuff.