Time for some investigative work it seems. This morning I tested around with it and have gathered a couple clues.
When the ball goes into the saucer the trex comes down and swallows it as normal. It then comes back down and up again but doesn't close its jaw. This is exactly what occurs when the trex is supposed to eat the ball from the saucer but the ball is removed before it can be swallowed.
Next I took a flathead and manually pressed and held down the saucer switch. The trex did its proper routine but this time it did not come down for a second bite. This makes me think something down the line after swallowing the ball is causing this issue. The only things after that are the trex subway switch and VUK. I tested the switches on both in the switch test and both appear to be properly operating.
I would guess the saucer switch may be faulty but I have doubts as after the first swallow the saucer switch uses the kicker to kick the ball out of the saucer. If there was a second false switch activation I would imagine the saucer would kick as opposed to send the trex down.
My next test though a PITA to setup properly due to all the balls is to lift the playfield and have the trex swallow the ball but stop the ball before it hits the subway switch and see how it reacts. Repeat but have the ball hit the subway switch but not the VUK and again observe the reaction.
My guess is that the VUK is rattling something causing the trex to go down but as of right now that's just a total guess.