I'm not sure if this is a Vault issue or GM but either way it's making getPlayerGroups(player) useless for GM.

When I do getPlayerGroups(player) or getPlayerGroups(world, playerName) it doesnt only return the current group as stated in the users.yml but also every inherited group connected to that group.

users:
Armar:
subgroups: []
permissions: []
group: Local

getPlayerGroups(player) = {Local, Default, g:local, g:default}

this is intended. The GM author programmed it this way.

I understand, but this makes getPlayerGroups completely useless as you don't really know what result it's going to give you. Do you have any idea on how to work around this ?
The thing I'm trying to accomplish is allowing my Autorank plugin to also be able to work with multiple groups. For example when a player was given the Donator rank, their previous rank stopped being changed by autorank because I used getPrimaryGroup. So getPlayerGroups seemed to fix that at first :S

not much I can do, the method in GM returns all groups inherited. I would want it to anyway since that's what the method implies.

Then is there any way for me to know what permissions plugin vault was hooked in to so I can disable the multiple group support on GM ?

yup, it's just leveraging the Bukkit ServiceManager interface for this. using getRegistrations instead of getProvider() will list all registered instead of getting the first one.