Seems that whenever I do anything with triggers in my map it says "Something bad happened, would you like to save a diagnostic file?" I can just continue working and ignore it, It will still seem to work properly, it's only if I go Yes or No on the error window that it closes.

So it doesn't seem to be a really huge issue, but I'm wondering if there's a way to stop this from happening because I think this error disables key shortcuts like CTRL-S, X, V, C, etc.

If you can go back to an older version of your map where this hasn't happened.
You can also try to save the map with another advanced map editor, like Starforge, and then go back to ScmDraft. Be sure to make a backup first since this can potentially corrupt your map.
Not sure if this can have something to do with it, but it's worth a shot if the other methods weren't successful: Delete/Rename the backup database in your ScmDraft folder. Should be the largest file.