I would say report the problem to the seller. First, make sure there are no adhesive stickers that need to be peeled off the battery or the battery compartment.
If bought from 'unauthorized' source, there is always a chance the battery was replaced and is not OEM.
Are there any plastic tabs or left-over tabs from lid manufacturing process that may impede a flush battery installation? If so, you could "shave" or sand these off and try aligning the battery again. If not, you might want to return the phone (or get an aftermarket lid, whichever works for you).