See https://github.com/Cryptic-Mushroom/The-Midnight/issues/312
The issue seems to lie on Better Foliage's end. Some of the foliage in The Midnight has a box around it with the missing texture symbols. The author seems to think it is an issue with emissive textures.

For now the solution for me is to disable Better Foliage which is a shame. Hopefully there can be a fix.

I'm having the exact same issue in 1.12.2; I'd like to just disable BetterFoliage for that foliage specifically using the blacklist feature, but I'm unsure how to go about doing so since the blacklist doesn't utilize item IDs.