If the transfer is aborted/closed or starved of bandwidth for a while the server will close the connection and ioNinja will receive the uploaderror event which usually results in the crc-mismatch error for dirs with an sfv in them... That's working as intended. I personally disable that error notice in the bot config file from showing up in channel because some users trigger it a lot. I think what happens is you'll get that error if the user tries sending a file but can't connect either because of network issues or because the sending user didn't have credits on the source site if they are FXP'ing.
No idea on why you'd see a bad file showing up the system dir though. Since it's got a .bad extension I'm guessing it's an ioNinja error. By default ioNinja deletes bad uploaded files rather than renaming them .bad so that might not be a well tested option...
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