This is fair. If somebody stumbles across this thinking it is how you intended it to be displayed, I can understand you'd be unhappy. We should make it clearer that we're just a conversion tool, not a source.
If you want us to remove your paper and just point at the PDF, we're happy to do so. My email's in my profile if you don't want to post the broken render here!
Thank you for your reply. Ideally I’d prefer for you to respect the license associated to each paper and only re-compile and re-host if the license actually allows you to do that (i.e. CC0, CC-BY, CC-BY-SA and maybe CC-BY-NC-SA, depending on whether you think you act commercially).
I also don’t want to keep tabs on every arXiv rehoster and inform them manually by e-mail every time a new paper goes up.
May I ask why this was not done together with the arXiv itself? I.e. have the infrastructure run there, let authors check the HTML render at the same time as the PDF render and then, if the author thinks they look ok, have them show directly on the abstracts page? This would even avoid all your license problems, as the arXiv already has the corresponding license!
If you want us to remove your paper and just point at the PDF, we're happy to do so. My email's in my profile if you don't want to post the broken render here!