Bukkit

Please make an option so users are able to activate pressure plates, buttons, open doors, etc. in areas where they cannot place nor remove blocks.

ProtectionStones uses WorldGuard for all it's protection, if you have the Use Flag set to deny and players who aren't owners or members are able to use those items then either you have a region problem where there are over-lapping regions which are over-riding the Use Flag (normally due to the parent child settings or priority levels) or you have a problem with WorldGuard itself.

Check first that you are only in one region, no overlaps, then make sure the Use Flag is set to deny, then make sure the player trying to use the restricted items isn't a member, WG also supports groups, so make sure you didn't add groups of players to the region that includes the players you believe are restricted from use.