@Zachary Whyte Thank you for your response. That won't be necessary, I went back on a previous save and played on from there.
To note, I did not have any custom database or external files loaded whatsoever. Not even logopacks, facepacks, nothing at all. The save was purely with the base game, and I have in fact never used any external files with FM23.
So, the problem is purely an issue with base game. And through my own testing and from what I have read from others, the problem is this:
When signing a player who is not set to join right away and does not currently have a club, you have the option to "Have the player join on trial until the move". Selecting this may cause the player to become duplicated when they do eventually join the club, It does not happen every time, but it happened to me 3/6 times, so the issue is prevalent. A fix is to drop the player down to the youth team and recall them, however this is not a solution when managing a side that does not have a youth team (like Atletico Ottawa, whom I was managing).
Having reloaded the save to an earlier point and not selecting the "Have the player join on trial until the move" option, there was no issue.
To restate, this is a prevalent and game-breaking issue in the base game, and should be addressed ASAP.