I live in a townhouse. There is a shared breezeway that allows both us and our neighbours access to the backyard through the garage (the garages are at the front of the townhouses, so the breezway is like at 20 foot long alley). The roof covers the entire breezeway (about 20-25 feet above the ground). Close to the garage in the breezeway there is a non-fuctional piece of roof about 10 feet off the ground. Pigeons like to roost on this piece of roof so I built spikes out of chicken wire and attached it to the roof by using wire guides (with nails on either side of the U). Now I'm worried that I shouldn't have nailed into my roof. Is it okay to nail into a peice of roof that is protected from rain/snow like this is?

Yes. In the future you should use a constuction adhesive from a calking tube, if the roofing is exposed to the weather.