Yep. This is one of those things that I could see happening, as I have a somewhat similar story.
Lonng version - Tl;dr at the bottom: (Warning: if you don’t know how to play Settlers of Catan the story will probably be confusing; hell, even if you do know how to play, it may be confusing because I'm writing this half asleep).
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My brother is color blind (he can't distinguish a difference between green and red). Anyway, we play Settlers of Catan often. Then we got the 5-6 players expansion.
The very first time we used the expansion (we had 6 people playing), I noticed my color-blind brother (who I’ll call C-B) often putting the Knight on me when he rolled a 7. (I was green.) Okay, I'm used to being picked on when it comes to Settlers. Later on in the game, C-B puts the Knight on my other brother (who was Red and in bad position, only 3 points). He responds:
“WTF C-B?! Why do you keep putting the Knight on me? I realized then that the times my CB wasn't putting the Knight on me, he was in fact putting it on this brother. Put it on someone who is actually winning!”
C-B: ”What are you talking about? You have at least 8 points!”
Other brother: ”Huh?! No, I have just 3.”
C-B: “No, look, you’ve got Longest Road, 1 city, 3 settlements, and a Gd-knows-what Development Card.”
And that's when we all realized what was going on. When C-B looked at the board he saw green and red as one person's pieces. (It sure didn't help that they were near each other) We never associated Settlers as a game that could be an issue for C-B because it never was; the original Settlers comes with red, orange, white, and blue pieces, the expansion comes with green and brown.
In order to finish the game, each time it was his turn we had to point out who each red and green road/settlement/city belonged to. Lots of fun. (First-world problems, I know.)
End result: we no longer use green and red at the same time if he's going to be playing.
Tl;dr: Played Settlers with the Expansion set for the first time, which has green pieces to go along with the original version's red pieces. Brother kept thinking whoever was green/red was winning and tried to block those spots. Other brother who was red and losing got frustrated, asked him what's the deal. We then realized my color-blind brother thought the red and green pieces on the board belonged to one player, giving that player the most points.