The extraordinarily frustrating case is where you're working on a repository that has multiple files that differ only by case. Git will check out one of them, then overwrite it with the other.

The Linux kernel is one of them: several of the headers that get installed to /usr/include/linux/netfilter have conflicts on a case-insensitive filesystem. https://github.com/torvalds/linux/tree/master/include/uapi/l...

Debhelper used to be one of those until I convinced them to change it: they had a Debian/ directory for the Perl module Debian::Debhelper as well as a debian/ directory for the packaging metadata. https://bugs.debian.org/873043

(I suspect I'm a little unusual in wanting to have checkouts of Linux and Debhelper on my Mac homedir.)