There are quite a few examples, but here's two that have affected me

1)pstcol has to be loaded before graphicx (I forget the reason but it just does)

2) if I use pdftricks I have to unset the "clipbox" command because it conflicts with the one in adjustbox.

As you say in another comment, given how latex reports errors debugging these can be a Fun time.

It's been a while, but I vaguely remember that the hyperref LaTeX package for making URLs didn't play nicely with certain other packages -- possibly with one of the citation packages.

Sorry I can't be more specific. I definitely have memories of reordering \usepackage{} statements until "it worked"...

This is correct. In fact there is a highly upvoted question about it on TeX Stack Exchange: <https://tex.stackexchange.com/q/1863>.

See also <https://latex.org/forum/viewtopic.php?t=25156>.