Not sure exactly what triggers this, but I have twice now seen two ships listed on the Sell list when there should only be one. Both times I saw this I was on a trade retrieval mission, docked at the station I was to retrieve from with a hold full of non-mission cargo, so the mission cargo was placed in the station hold, I unloaded the non-mission cargo, loaded the mission cargo, and switched to the sell tab to sell the non-mission cargo, and saw my ship listed twice.

Were both of them highlighted in red?

Meaning they couldn't be sold? Yes. Another thing I forgot to mention, was it only listed them both when I also had the non-misison cargo listed on the sell tab as well; after I sold the non-mission cargo, and switched to another tab & then back to the sell tab, it was only listed once.