So I'm wondering if anyone from the community knows what could possibly cause this as well as possible solutions.
As richvh said, you probably have a stray pixel somewhere. Easiest way to find out (using Gimp, but probably for photoshop as well), is to use the select by colour tool (zero threshold), select the province in question, and then File>Create>By Clipboard. The stray pixel(s) should stick out quite easily.
I'm new to modding, so this is probably an idiot question, but:
I set up a mod with the intent of adding in several new cultures. In order to actually get the cultures in the game, I scrubbed all the province and title history (not characters though), then copied province history from vanilla into the mod and edited the appropriate provinces' files so that my new cultures would show up in them in 769. I also created a text file under history/characters which then contained a few test characters, each belonging to one of my new cultures, then I added a couple of files to history/titles for the provinces these characters would own for a quick test run. I edited in each of those titles' holders at 769, then copied over the vanilla history files for a random county in the middle of Bumfuck Nowhere, Africa, so I wouldn't have issues with not having any characters at 1066.
For some reason, though, every single county that I had assigned to the test characters was instead given to one guy, the guy with the highest number for his ID (so therefore the "last" one). I had one count holding six counties when instead there should have been six characters with one county each. What's going wrong here?
Are your county histories pointing to the correct character and not all just to the one guy? Does each character have their own unique character id?