A while back, I installed members - and activated it on my main site; and network wide.
Now plugins that Create Permissions when an Admin Activates them are negatively affected on new sites in my Multisite Install.
I can retroactively add permissions on each subsite, but that is not practical.
Note - even with members deactivated, it seems new plugins are affected.
One of the most common ones are bbPress - when an admin in the multisite activates bbPress, they cannot view/edit/create forums, etc.