The large Kaylon fleet is directly behind the Orville while traveling towards Earth at quantum speed. When Gordon and Kelly pilot the shuttle out of the rear of the ship, they should be headed straight into a swarm of Kaylon ships, yet no Kaylon ships are seen at all.
The code for the shuttle bay door is ALPHA-ONE-FOUR-OMEGA-SIX.
When Ty reached the shuttle bay door, he only presses 3 buttons.
At the airlock, when Primary is sending Isaac to the bridge, you can faintly see Graham Hamilton's mouth moving under the face shield.
The Orville is equipped with two shuttles. The shuttle bay is demarcated with spaces for them on the floors and walls. Only one is present in the shuttle bay while the crew is held captive there (in reality, only one shuttle prop was constructed for the show, so for a second to appear, it would need to be added with expensive special effect shots, taxing the already-stretched budget for this episode).
The Kaylon aboard the Orville are made aware of the approach of a Union vessel. Several minutes later, the bridge crew is escorted to the Orville's bridge and identify the USS Roosevelt coming out of quantum. The Orville has been shown to have very poor ability to detect ships approaching at quantum speed, and the distance the Roosevelt would have traveled at that speed during that time would have put their starting point well beyond the Orville's usual sensor range. The Orville should not have had so much advanced warning of the Roosevelt's approach.
Gordon explains the establishment of a "pee corner" to the rest of the command crew, in lieu of proper lavatory facilities. As urine is a liquid and the shuttle bay floor is flat, urine would not stay confined to a single corner, especially not with the volumes produced by multiple crew members making use of the pee corner.
Yaphit and Ty are the only ones small enough to fit through the conduit leading out of the shuttle bay. It makes no sense for a ship built and maintained by fully grown adult humanoids to have lengthy conduits too small for crewmen to access.
The crew establishes a "pee corner" in the shuttle bay for going to the bathroom while held captive. Crewmembers have been shown taking the shuttles on trips that last many hours, sometimes longer. It would stand to reason that there must be some form of lavatory built into the shuttles. The crew could have used the shuttle's facilities rather than going on the shuttle bay floor.
When formulating a plan to send a message to Union Central, Yaphit points out that none of the rest of the crew can fit through the conduit, as it's "only half a meter wide." The conduit shows is much smaller than half a meter.