@sabbatical I'm so tempted to say "all of them" but there's a few favourites:

Title case for some things, sentence case for others (either all the same or don't change case, IMO)

No period after a URL in citations but other fields of a citation should have a period.

Varying indent rules depending on what part of a paper you're in.

And above all, no footnotes! I'd much rather have footnotes than endnotes.