PDF libraries generally assume standard 8.5" x11" paper. This means that page resolutions can definitely be wrong.
There are a few options. The best is if you are the one creating the PDF, to make sure you are creating it at the same size as your actual label. Say you are using MS Word to create a PDF, you need to make sure the full original document size is 4"x6" or whatever your label really is.
The other option is to use some tools to scale the image properly. PDF tools are very variable and some are much better than others. I'm not sure what scaling options are available in the iOS native library.