I spoke to Trask and decided I'd look at his evidence back on Harlow's base.
I went and got the evidence, spoke to Harlow and called him out. He decided I was compromised and automatically we went into combat mode. I killed him and fought my way out of the base. I spoke to him right after killing Harlow and we did the dialog about not knowing what goes on in someone's skull and that I think he's better than that regarding breaking their moral code for bits. This triggered quest completion...
The quest log however marked itself as completed despite me not speaking to Felix on the ship. The quest log leaves off that Felix wants to speak with me still but it's completed and Felix doesn't engage in conversation outside of the default leave my crew or go back to the ship.
Also of note, the quest says that I killed Harlow on a whim, which is definitely not what happened.