If you are using a YubiKey NEO on Windows, you may experience Windows playing the USB disconnect/reconnect notification sounds. This is caused by the NEO disconnecting and reconnecting the smart card so that it can switch to the OTP and FIDO modes. If you want to prevent this, you can disable the connection modes you do not use (EG: CCID) or disable the notification sound in the Windows settings.
Windows Plays the Device Disconnect Notification When Using the YubiKey NEO
Erin