It's possible that it could have come that way, sure. Please also check for partial downloads on your sd card, good idea to delete any of those you find.
As you know on your PC, your hard disk can get dirty over time with things that chkdsk can clear up. If it's a really bad situation, your PC may ask if you want to run that when it reboots sometimes.
Android (Linux) runs a similar process at bootup. Rather than ask you questions like chkdsk, it just handles cleanup silently and it sweeps the dust into LOST.DIR, so to speak.