Happened to me as well, many times in the beginning. I would use the USB cord to transfer files but it would crawl on transfer speed. So I would unmount SD then take out use an adapter and transfer that way. When I'd put back it would sometimes say that. I put back on adapter and into PC and sometimes (only a few times) and it would have to check for errors.
Lately I haven't had any issues (knock on wood lol), and have been using the cable for transfers just fine and sometimes use the adapter and still works. Thought it had to be a bug or something cause I would just pop out and put in a couple times (if needed) and then the media scanner would work.
But running MegaTron latest A.T.M., and was using that ROM when I had issues as well. But I have since then re-flashed the ROM and partitioned the EXT4 partition, so not sure if it was just the re-flash or the card. I only have an 8gb class 4 micro SD as of now and all is well ATM.