I've done the same to my iphone 5. Replaced the battery and must have scratched something. I was extra careful as I just spent 2 days soldering together a complicated kit, but I guess I wasn't careful enough!
Went to the Apple store today and they checked out the phone. Told me the battery reads as null. Told me there was logic board damage but no further info. Guy suggested to wait it out for a while as its more or less working now.
Its annoying but at least I know the new battery is keeping a longer charge as my old one was draining quite quickly.