I am not sure; perhaps indeed this is something with the GnuPG. Could you provide the exact steps for the local reproduction?
Nitrokey App is sending the PIN as-is to the smart card, without any mangling except providing it in the UTF-8.
If you are interested in further debugging, I plan to set up debug log for the scdaemon, the GnuPG bridge to the smart card, and we should catch the problem there.