I've built and installed Emacs HEAD (de8837599112608feecea65a1e520866bc171569) on a fresh Linux laptop. When I add MELPA as a package source and try to install certain packages from it (e.g. toml-mode, dark-souls), I see something like this in *Messages*:
Most other packages from MELPA, like rtags, are installed without issue. I haven't yet seen an issue installing a package from GNU ELPA (though I haven't tried too many of them).
As far as I can tell, for both successful and failing cases, the .el file downloaded from the given URL ends in a trailing newline.