Something very strange is going on. I did another test where I deleted everything inside the hex (including scripts), so it's just a RectTransform and a CanvasRenderer. It took over 1000 hexes, but I was able to reproduce the bug by duplicating these empty hexes. I then had weird behavior where disabling them did not make the quads show up again - I had to actually delete them from the scene before the quads would show up again.
So I've reduced this problem down to: Main Canvas --> Container with ONLY RectTransform --> Container with ONLY RectTransform (Image, script, canvas group all disabled) --> Container with ONLY RectTransform --> Hex object with only RectTransform and CanvasRenderer. All scripts on or interacting with any of these objects have been removed or disabled. The main canvas does have a canvas scaler, but I disabled that to no effect. I also tried disabling everything except the STM on the object that has the quads.
Here's my STM settings:
