I assume you have pcscd installed, along with the file /etc/libccid_Info.plist (this probably needs to be patched with the device ID for the YubiKey 4 / Nano with CCID only enabled
('0x1050', '0x0404', 'Yubico Yubikey 4 CCID')
I would go to this post (
viewtopic.php?f=26&t=1609#p6270) and enter the command from step 8. This will patch libccid_Info.plist, as well as add the udev rule for U2F in Linux (which it sounds like you don't really need, but it certainly won't hurt anything). You can view what the command actually does here (
https://raw.githubusercontent.com/Yubic ... -ccid-udev) Afterwards, reboot and try again.
Assuming this works, you may want to try and swap configuration slots with the YubiKey Personalization Tool (if you have the PPA added, "sudo apt-get install yubikey-personalization-gui"). You can go to Settings > Update Settings, select a configuration slot, and click "Swap." This will at least require that you tap the Nano longer before the OTP is sent. Of course this all requires that OTP mode be enabled, as most of our tools require OTP to be enabled to order to recognize the YubiKey.