There have been some ongoing changes in the LEF files; the SkyWater standard cells have some inconsistencies between the libraries, and since we had a single script to generate LEF from magic, the files produced from magic for some of the libraries were conflicting with the SkyWater cells. It may be better to use only the files generated from Magic, although there are a few problems with those related to missing information that needs to be passed to magic from somewhere. These things are getting (slowly) corrected in the repository files. You might try changing the line you cite above to

lef %l/latest/cells/*/*.*.lef compile-only \

to use only the .magic.lef files, and see if the result works better.

@User I tried that and it cause pin access issues in tritonRoute, so I'll stick to the .lef files for now.