I just tried to reproduce your observations and it turned out to be an not reproductive issue which might be related to directory watching by the OS and other applications (e.g. indexing, anti-virus,...)
Boxcryptor by default automatically adds thumb drives and external drives as locations, and exposes them to services mentioned above. So, if Rufus tries to gain exclusive access to your USB stick while one of those services holds any locks on the drive, Rufus might throw an error.
To encounter this problem you could go to Boxcryptor Settings -> Advanced -> Show more settings and uncheck "Auto detect removable drives". Boxcryptor will no longer add your USB drive as a location what might reduce the number off access requests on that device.