This could look like a corrupted filesystem, due to having removed the USB key without first having the OS eject it.
USB writes are async. The OS may tell you that the copy process to the USB key is done and OK, but it lies. That's why the key still blinks for a while afterwards, and that's why you should never, never remove the key before ejecting it by whatever means the OS offer you.
If you always ejected the key properly... then I have no idea right now.
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