Can you share a few examples of failures? There may be missing fonts / configs between the server and what arXiv runs to generate PDFs.
E.g. arXiv:gr-qc/9504004, arXiv:1512.01236, arXiv:2102.06824
Thanks for those examples. The first one errors out because there's no content in v1 of the paper (admittedly, I need better error messages). I've fixed the other two.