Theory 1) Azmuth Was Actually Behind This
From what we know, Azmuth doesn't prepare for possibilities but he added the Failsafe to the Omnitrix which comes in handy in most of the situations, so what if he is secretly planning for the possibilites? Maybe Azmuth knew that Albedo was going to steal the Omnitrix Core and didn't added the Failsafe?
Theory 2) Ultimatrix Can See the Future
This kinda doesn't makes sense but it's a theory after all. What if Ultimatrix can see the future and knew that Ben was going to be revived?
Theory 3) The Ultimatrix is Simply Weak Against Soul Based Attacks
Ultimatrix might be weak against soul based attacks since Charmcaster killed Ben that way.