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I'm running Ubuntu Server 12.04, and basically found out that a couple of files aren't behaving like they should.

The file name is r.-1.-1.mca, and I've tried using this terminal command sudo cp r.-1.-1.mca ../

The hard drive is working/thinking for a while, then spits this back out:

cp: reading `r.-1.-1.mca': Input/output error
cp: failed to extend `../r.-1.-1.mca': Input/output error

I have another file behaving like this. My guess is that these files are corrupt, so I tried running the server in recovery mode and it told me to check the file system. However, it didn't come up with any errors.

Is there a way to repair these files so I can use them normally again?

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Most likely that error is due to an bad sector on your hard drive. any errors in dmesg ? You can also try running testdisk. –  bodhi.zazen Jun 28 '13 at 20:39
dmesg gives quite a few errors –  QxQ Jun 28 '13 at 20:50
Post them. I advise you back up your data ASAP. You can not fix bad sectors, you can re-format the drive and buy some time. I had a hard disk last several years once that way, had to format it several times, and one day it failed with no further warning. Had a back up of all my data, so no big loss, just being lazy. If you value the server, replace the HD. –  bodhi.zazen Jun 28 '13 at 20:55
I don't know what information is important. here is all the output: pastebin.com/dnPaWwaB –  QxQ Jun 28 '13 at 21:00
These messages "[ 850.108421] sd 0:0:0:0: [sda] Add. Sense: Unrecovered read error - auto reallocate failed" seem to indicate your hard drive is failing. –  bodhi.zazen Jun 28 '13 at 21:02
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