Ahh! so I'm not the only one in this case, I have got the exact same problem than you about this automatic filename test.
I forgot to talk about it, but I use Minify Manual where I put some JS and CSS files manually.
And when I put the jquery.js from wp-include in the minify box, all scripts using jquery don't work anymore. So I had to minify only some basic scripts that are using no other libraries, and I still get this error message.
PS: I'm using Cloudflare, I didn't check if disabling it remove this error message, but I don't think so.