If I encrypt or decrypt a file on a USB stick, I cannot eject it, as Windows always says it is in use. AxCrypt appears to keep hold of it after the operation. I’ve found this issue on two machines, a Windows 8 and a Windows 10. I’ve just had to wait a while and pull the stick out, hoping the writing to it is complete.
I am not sure that it’s actually AxCrypt as such holding on to the USB drive. There are several mechanisms at work, one of them being Windows caching of data being written to a USB drive.
You can always try and really exit AxCrypt to see if it makes a difference. There are also various utilties and built-in windows functions to see just what program is locking a file or drive. Windows Resource Monitor and wholockme are two.