Is there some file that is completely fine that the antivirus could reasonably confuse with a trojan? When installing the game the antivirus singled out a file and got rid of it. I didn't look too into it at the time because it was late but the antivirus is pretty sure nothing is wrong with the system now but I was wondering if anyone could explain this.
Always close your AV before installing games, because as you have already experienced, not doing so can lead to installation problems, which can and most possibly will lead to problems while playing the game, such as CTDs etc.
As for the reasons why this may happened as well as some general information regarding AV programs and false positives, check out the following links: https://www.howtogeek.com/180162/how-to-tell-if-a-virus-is-actually-a-false-positive
Thank you very much for the advice, much appreciated.