It almost sounds like the PBX isn't releasing the E&M channel when a call is hung up. If the E&M channel is hung up, then the associated PRI call should be released as well - and vice versa.
This can be a difficult issue to trouble-shoot. Since you don't know which channel any of the calls are on, you'll have to set up the ATLAS to log the events, and then set up a Syslog Server to save it to a file on your PC.
Although the "Adtran Utilities" are no longer available or supported (it was written for Windows 95) the ATLAS configuration in this guide goes through configuring the ATLAS: https://supportforums.adtran.com/docs/DOC-1391
Under the SYSTEM CONFIG you can go into EVENT LOGGING and you'll want to set the following events to INFO:
DP Outgoing Signalling
You may also want to set ISDN L2 FORMATTED to INFO, but this is VERY verbose, and if you don't need the ISDN D-channel message details, then it hopefully won't be needed.
On the E&M T1, the Robbed Bit Signaling (RBS) will be displayed as TxABCD and RxABCD, and should be either 00 or 0F for all zeros or 1111. The "Tx" and "Rx" is with respect to the ATLAS. So if it shows RxABCD: 0f and TxABCD: 00, then the PBX has seized the channel and should be sending the DTMF digits to dial. If the RxABCD: 0f and TxABCD: 0f then the call has been answered. After this, if the Tx or Rx changes to "00" then one side or the other has hung up the call, and the other should then go to "00".
(I may have the Rx/Tx order backwards, but it is still with respect to the ATLAS - either the ATLAS is transmitting, or receiving the change.)
Hope this helps,