OS X keeps a separate trash file for each connected drive: If you use OS X to delete stuff on your flash drive, it doesn't copy everything into your hard drive's , it places it into the flash drive's trash.
It creates a hidden .trash file. This file is the same size as the file you are deleting, if fact it is the same file, just renamed. The OS does this so you can utilize the "Put It Back" command. You can empty the flash drives trash by selecting it in the finder and then selecting empty trash from the Finder menu. (or hit Shift+Command+Backspace).
To avoid this issue, when using a MAC OS always empty the recycle bin prior to removing the flash drive