the permissions in the groups folder are you basic permissions(what a player can do in the unprotected world).
then you have area permissions that are assigned to a player(Owner). areas also have a default permission witch is active in an area that any player does not own. since your default permission is to restrict non owners you want to block pretty much every thing in this permission. once an area is created you must set the default permissions and add an owner.
there is a hierarchy to the permissions as well.
if a player is not in an area it uses group permissions
if a player is in an area they do NOT own the areas default permission is used .if this is not set it uses the players group permissions witch is where i think you are having your issue as they are destroying areas. without this set they are basicly able to act as they are not even in an area.
if a player is in an area they own it uses whatever permissions group the owner is assigned to
for example. i have a cities areas permissions. when i set this are the default area players can do things like open doors but not chests.
another example. i have pvp areas. the areas default permission allows pvp but enables loose items on death. so even if a player is in a group permission that does not allow for pvp its of overridden when in the pvp area.