If you can't find your agent-to-agent call in the logs then make sure it wasn't an outgoing or incoming call to start with.
The call logs show the direction of a call eg; Incoming, outgoing or Agent-to-agent. A call is only an agent-to-agent call if it began as an agent-to-agent call ie; the call was made to an agent from the "Make call" option in the Call Centre :
If your call started as an outgoing or incoming call that you put on hold to talk to another agent, then the call will still show as an outgoing or incoming call in the logs not an agent-to-agent call.