As it turns out, there might be something wrong with Netlify trying to fetch files from Git LFS. Only the extensions listed here: build-image/buildbot-git-config at focal · netlify/build-image · GitHub seem to be correctly fetched. Any custom extensions that you would add using GIT_LFS_FETCH_INCLUDE, do not seem to work at the moment.
This as been escalated to the devs and we would let you know as things develop.