bug when changing pets (Pillars of Eternity)

Pets cannot be changed, perhaps you mean those Everushki from which there is no use? (space pig, black cat, pink pig, labrador, albino dragon, etc.) bugs usually occur due to conflicts in the parameters of the animal should not affect, but perhaps another item conflicts.

look at the main attack, change pets among themselves and it grows

As far as I know, pets in this game are a little more useless than not at all.

Piglet Peter
I agree because of them often starts a fight if you sneak past opponents.

XeqtR
change the repack animals do not give any increase to the parameters and do not affect them in any way

Official GOG, sort of. so that the animals give an increase. you need to do such actions - you put 1, exit the inventory, you go in, you put the second one, and so you cycle, up to 170 it turns out, then it is reset to zero.