Hello,
Thank you for your query at DoctorSpring.com
Yes it seems to be like bits of the digested magnet, and from your description it was not too big either, so it should pass on it's own as the doctor in ER told you.
He is probably fussy because of the abdominal discomfort it is causing him.
It is better to get an X-RAY done to confirm that the bits passed. I will advise you to wait today, and observe him. If he keeps getting better then there is no further reason to worry. If he still acts fussy then you can just go back to the ER and get an X-RAY done to see if there is any foreign substance.
Regards.