Hello there.
I've got a 3,5" HDD USB enclosure externally powered connected to my RPi (model B). A while back I was having some input/output errors, and the HDD (Samsung) would get quite warm, so I thought the HDD was dying and bought a replacement (WD Blue). Just after the backup all the files on the original HDD disappeared, so I thought the problem was indeed with the HDD.
After I changed the HDDs, the first difference I noticed was when I made an "ls" on the command line. With the original HDD, most of the folders would appear with a green color around the name that would make it almost illegible. With the new HDD, everything was normal, just the plain text with no weird colors.
New HDD installed, it was time for some torrent downloading. I downloaded and uploaded a few torrents a the same time (around 20, I guess), and I think that it might have been my problem: after a few days, I started getting input/output errors again, needing to reboot the RPi, and had the same strange green color around the folders' name when I did a "ls" at the root of the HDD (which was and is ext4 formatted, btw).
Now I'm wondering what might be my problem: would it be too many files / access for the RPi to handle at the same time (transmission was a little unresponsive)? Are the HDD and/or enclosure just not fitted to RPi? Could it be a faulty SD card (I've read that a change of SD card did the trick in one case)? If the latter might be true, is it better to make a clean install or could I make a clone of the current SD?