Most likely you have a deleted item/event/place with a command still linking to it ( them ).
Check your events, if you see a (?) some where, redirect the event path to something that exists. Just check your events in the area where you get that message for any thing that conects to a deleted item/place/whatever.
Example: If you have an event that teleports you to area 1a, then you erase area 1a, the game will still try to teleport you to that area, which it cannot because it does not exist. You must change the event to warp you to an existing place. Same goes for items.
Oh, the (?) is for RPGmaker 2k3. If your not using that it may be different, but the same principal still applies.