The issue is that their LaTeX installation is fairly old, so there's a real chance of running into old bugs that have long since been fixed. It's a bit tiresome to work around those. I've had issues with their pgfplots version and had to resort to compiling the figures to pdf locally and including those.
Nah, I mean that it is a pain to upload error-free files. Due to dependencies with libraries and other reasons, a file that compiles in your computer often fails to compile in the arxiv.