I don't see any reason why you were told to remove the headphones from around your neck, I have never told anyone to do that.

Stowing items in the seat pocket in the exit row is fine, as long as they are not bulky and stick out. For example:

Book ^
Paper ^
iPod/MP3 Player ^

Laptop
One of those leather folio zip up folders
Bag containing sandwich, bottle of water, packet of crisps

Anything that sticks out prominently and may get in the way or be large enough to be knocked out of the seat pocket and cause an obstruction will have to be stowed somewhere else.