Recreated the issue - there was an 8 block in the top left (0,0) which is why the 8 block at (1,1) went grey. I deleted the top left 8 block using a 1 block, but the 8 block at (1,1) is still grey even though there aren't any more duplicates in range. 
Viewing post in Paint Me Something, Will You? jam comments
Oh right, that must be it then. Briefly before submission I did noticed something strange with the score or the penalty system, but I couldn't figure out what or why, so at the last minutes I wrote a vague warning on the game's page that there would be bugs. You put so much thought into the game and even helped me find the bug and I really appreciate that!