This is not really a bug, and I'm not sure how much we should work around incorrectly constructed files.
But files with _FillValue on coordinate variables do turn up in the wild: https://discourse.julialang.org/t/visualising-netcdf-using-raster-jl/85761
Currently that error passes through NCDatasets.jl, outputting a dimension variable with Missing in the Union type. Rasters.jl does not currently handle this, assuming it wouldn't happen. I'm not sure where it is best deal with it, it can also be in Rasters.jl - but I'm making this issue so it is know about here as well.