It ended up being a steam issue with a particular mod I guess. "Krakens Better Dinos" is what I was using, and according to the creator steam isn't sending proper update notifications or something like that, so the mod won't auto update sometimes.
Basically I was assuming that mods auto update when you restart the server, however I have reset the server a few times and every time I try to connect it says to ensure that I'm running the latest version of the mods. Is there a way to manually update mods or to force an update for them? Any help is appreciated, thank you.