Yes, the whole thing with Cutter in 3.3 was badly handled. It would have made more sense if they could have shown that Becker was obviously unable to go after him for some reason - either he was injured, or he was heavily involved with something else that was important, such as overseeing getting other survivors out of the building.

The writers are far too reliant on having Becker conveniently vanish for no reason when they want the civilain scientists to be doing the dangerous stuff, unfortunately.