He can't get them all if there are Dark Aeons. He'll have to do with the ones he has, or Yojimbo his way through.
you CAN get every of the monster without fighting dark aeons your talking about the magus sisters right?

you can walk past them to get to the mushroom rock road. without being chased by the magus sisters


if your talking about another one then i must have axidently killed one on the way

valefor = no need to go into the village
ifrit= can get every monster without going to him
ixion= you need to talk to the gaurd at the tower to get him to apear
shiva= temple is not needed for monster capturing
bahamut = what do you want to capture at the zanarkand dome
yojimbo= no need to fight him even when he apears
anima= also your own choise
magus sisters= you can get past the first to summoners by walking on the far left of the screen you can get every monster from that part in the way to the save sphere (aurons masamune is also doable) then catch everything on the rock road (those birds are most found at the end of it near the elevator.

so wich one did i miss