The configuration of ssh vs https can break a lot of workflows, the inability to (reliably) track a branch from a submodule can make maintenance a pain, I've never really figured out how to reasonably do a rebase in the presence of gitmodules changes on both branches, github actions had broken support for submodules for quite awhile... just to name a few.

There's not one giant issue with submodules. There are dozens of small annoyances and footguns. I have yet to see a problem that is better solved by git submodules that can't be solved another way.