The tamed ones may try to go back to their spawn ; the bred ones will stay there. As long as you can breed some and kill the old ones, this problem should sort out by itself. Or tame / breed them on the spot, and bring the offspring to your farm ? should work too.

The ones that spawn at night (wolves especially, 2 stars boars too, prolly ?) will try to run when day comes (they want to get out of sight to despawn) unless you manage to get them to eat some stuff and start the taming process before morning. They don't despawn anymore once taming is started. But if taming is not started at daylight, they won't eat anymore, they just try to run.