The git commands don't seem to quote the -C argument so any spaces in the project path will cause atlas to fail.
mkdir "a space"
cd "a space"
atlas init
atlas use neo
[Error] (atlas:resolved) not retrying lazy deferred packages; non-lazy dependencies are unsatisfiable for: a space
so for example the command when run manually would, no surprise, show:
git -C C:\tmp\a space\deps\neo log --format=%H HEAD -n1
fatal: cannot change to 'C:\tmp\a': No such file or directory