Krin and Kasumi do some story-related mission(s) so they disappear at least once during the game. Viktor does this as well, although this is made obvious when it happens... yes it's strange that they disappear from your Tablet of Stars just because they're busy, but that's how it works for this old game.
I got the same problems too... I need 3 people that supposed to join automatically... Can we fix it or we need to play again from the beginning? (Coz I'm almost finish the game, if I need to reset it all, I'm so gonna cry...)
did you read? they come back. you can certainly try 'fixing' it with code breaker by trying the character recruit codes, but i'm not sure if that will make them count since the game does know they are recruited but is disabling them temporarily... you'd have to know the game's logic to be sure.