I have found that if I allow a call to flow from Unity to my Route point (unity set to supervised transfer), as long as I let the transfer from Unity complete I can then redirect the call to a phone of my choice.
 
If I attempt the redirect as soon as the call arrives at the RP, not only does my redirect not work - which may be fair enough as I may have supplied callid/connection details that are out of date as the transfer is occurring but I can it appears stuff up the JTapi call model.
 
I say this because I get a platform exception in jtapi (attempt to redirect a call that does not exist), I get a CiscoTransferStartEv but not CiscoTransferEndEv and Jtapi from then on reports both the transfer call and final call in the model even after I have cleared the external call down.
The Jtapi test tool also shows the 2 hanging calls.
 
Any ideas? This is on CUCM 7.1

It is important to wait for media to setup before the Redirect, and there have been some fixed issues in this area in past JTAPI/UCM releases.  However I would not expect recent versions to exhibit any confused/unrecoverable behaviour with persistant state-machine discrepencies, such as you describe, even if the Redirect comes early.
If you are on a recent UCM version and would like us to investigate the problematic scenario, please open a case with CDN Developer Support and we'll take a look.