The quests says to go to the ship. Except I'm *already* on the ship

In Saints Row IV, there are side-quests that involve you travelling back onto the ship (leaving the simulation) and talking to a specific character before doing any activity (back in the simulation).

However, the strange thing is that I'm on the ship, all the rules of the ship applies (no superpowers, etc.) yet still.. It doesn't detect I'm on the ship.
I've noticed strangely is that there is a quest marker underneath the center console, which is inaccessible without no-clipping.

I've tried going back into the simulation and re-exiting it (even at different portals), and nothing happens. The game still thinks I'm "in" the simulation, and not on the ship.

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Anyways, here's a screenshot:
Defintely on the ship. http://cloud-4.steamusercontent.com/ugc/39738595549738561/294A21EAEB4EE8D299154724C9327925722593D4/

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Is there any way to trigger the action completion WITHOUT clipping?

Or, if there is no way to do it without clipping, how do I clip then? Or are there any alternate methods?