The thing that made me notice was my map icon mod that changes the colors of the map icons. Whenever I go to the map for the first time, it'll say my SkyUI is version 3.0 and it's outdated, but when I go to check skui itself in the mcm menu, it'll say that it's at version 4.1. However, checking the mcm menu, it says it's version 3.0. I'm so confused... I even tried uninstalling it and reinstalling it but to no avail.

We keep separate version numbers for both SkyUI and MCM. The idea was to keep them separated in theory even though they are bundled together.

And about your error: The map marker mod that changes colors is based on a file from SkyUI 3.0 and the author hasn't updated yet. Or maybe has and you have to download the latest version. You can disable the version check for the map menu in the SkyUI options (Advanced section).