I've also encountered that bug with grass replacement. I had some landfill in my save before the mod installation, and all that tiles is bugged now.
It doesn't happen for landfill tiles that is placed after the mod installation, though.
Steps to reproduce:
1) disable mod
2) place some landfill and save
3) enable mod
4) place any tiling over that "vanilla" landfill
5) mine that tiling and it's now grass tile instead of water
Also worth mentioning that tiles (stone bricks in my case), which were placed over landfill before the mod installation, properly replacing itself with water after mining.