I've used Capstar several times with Zoe (she's about 5.5 pounds) and have never had a reaction like what you described! In fact my parent's vet has said it's so safe you could use it every day (not that you should, but that you could). I've even said that I think it's a miracle pill whenever Zoe's gotten fleas (since whenever we visit my boyfriend's family she always gets fleas; even when she's on Frontline or she doesn't even set foot on their property).
That said, I'm sorry you had to deal with fleas AND a sick baby! I agree with the others, I would talk to a vet. I'd be concerned that it could have been a reaction or something! All in all just keep an eye on him. Hope everything works out!