So, I updated Malwarebytes today and ran a full-system scan (which I do about two times a week), and it picked up a positive for a trojan. Funny thing is, the thing it was claiming was a trojan was an old mod for a game I downloaded (It was the Darthmod for Shogun 2: Total War). Now, it was an older version of the mod that I downloaded last year and never used, so it obviously had been scanned by Malwarebytes many, many times. So at first I just figured it was a strange false-positive. But, I don't really know too much about the evil trickery used by malware. Is it possible that a malevolent file was downloaded onto my computer which then copied an existing file name and then replaced it? Or am I being paranoid? As a final piece of information for those of you unfamiliar with the mod, it is fan-made and contains an installer.
Either way, I let Malwarebytes remove it (as I wasn't using the original file anyways), but I'd like to know for future reference. Thank you for your time.