You are probably using programmed Auto-Intercom buttons to call the other extensions, as opposed to pressing Intercom and dialing the extension number.
When you lift the handset, the system gives you an outside line automatically, thinking that you intend to dial an outside number. When you are connected to an outside line and press an Auto-Intercom button, the system thinks you have an active call and are trying to transfer it to the extension programmed on the Auto-Intercom button, so the line goes on hold, and the display says Transfer: XX. You have your internal Intercom conversation, and hang up, the transfer completes, and the line that never had anything other than dial tone on it is transferred to the extension. Since nothing was dialed, it has timed out and the "howler" is on the line, trying to get your attention that you left a phone off hook and need to hang it up.
Sometimes this isn't a problem, it you go off hook and don't dial anything, after a few seconds of dial tone you get a busy signal, and some time later it automatically disconnects. Some telephone companies, especially cable companies and CLEC's using IAD's to deliver dial tone, can't program them to disconnect on no dial. They have enough problems programming them to disconnect when the outside party hangs up.
So the solution is to train yourself to press INTERCOM before you press the Auto-Intercom button, or program your phone to select Intercom first, and you manually select an available outside line when making a call.