Also having the issue. Opened an issue here:
Tested under Ubuntu 15, Fedora 24 and Debian 9
Moved my keys from a working setup under fedora24 to the nitrokey pro.
I can decrypt mails read them through enigmail, can sign files no prob.
Bug when it comes to generate keys... Under Debian 9:
Admin commands are allowed
Make off-card backup of encryption key? (Y/n) y
gpg: Note: keys are already stored on the card!
Replace existing keys? (y/N) y
What keysize do you want for the Signature key? (4096)
What keysize do you want for the Encryption key? (4096)
What keysize do you want for the Authentication key? (4096)
Please specify how long the key should be valid.
0 = key does not expire
<n> = key expires in n days
<n>w = key expires in n weeks
<n>m = key expires in n months
<n>y = key expires in n years
Key is valid for? (0) 3y
Key expires at Sun 07 Jun 2020 01:36:55 AM EDT
Is this correct? (y/N) y
GnuPG needs to construct a user ID to identify your key.
Real name: Test
You selected this USER-ID:
Change (N)ame, (C)omment, (E)mail or (O)kay/(Q)uit? O
gpg: key generation failed: Card error
Key generation failed: Card error
Nitrokey firmware version 0.7
gpg (GnuPG) 2.1.18
...Any guide to help troubleshoot further?