If Spugnoir is unable to initiate dialogue with his familiar after it has been summoned, he will be unable to put it away. If you have a save from before he chose a familiar, I would suggest loading that save and give him a Toad familiar, don't use the item to summon the familiar onto the map and just enjoy the 3HP it gives you. Toads are pretty bad in combat anyway.
I just had to check out what was going on now that I'm not at work. Any PC can tell Spugnoir's Familiar to pop back into his pack, Sougnoir himself cannot however as he is an NPC, he is incapable of initiating dialogue.
I think that might have something to do with my main character . When he summons his familiar Hawk its okay he talks and retrieves him but when I summon him again its instant death 125 damage point to him.