Looking at some code that is a bit older it looks like some of it uses
make-local-variable where it is not needed since the variables in question
are always buffer local. From that I draw the conclusion that the code in
Emacs uses make-variable-buffer-local more often now. Is not that the case?
make-variable-buffer-local has the following downsides:
1 - it cannot be reverted.
2 - it may be done too late.
3 - when you see `setq' it's not obvious that the setting is buffer-local
unless you remember seeing the call to make-variable-buffer-local.
The second problem may also explain what you're seeing: some code may
set a variable before the make-variable-buffer-local gets run.
It's actually "common" to introduce bugs this way, because people see
"this is automatically buffer-local" in the C-h v info, so they just use
`setq' without realizing that the setq may occur before the package
gets loaded.
make-variable-buffer-local is not evil, but make-local-variable is much
tamer and more explicit, and it works just as well in most cases.