Mild spoilers ahead for some of the post story content of Terran Armada.
Had an issue while playing last night which wasn't game breaking but was certainly annoying. Had Andreja as my companion and had her locked because of her loyalty mission. Delta then wanted to talk to me about its challenges to prove myself worthy as captain. This forced Delta to become my active companion and Andreja began walking back to my ship. Once I'd done Delta's challenge I tried to get Andreja back as my companion but she refused because I was busy with another companion, even though it was her I was supposedly locked to. So I ended up in a weird situation where she was and wasn't following me!
What this meant in practice is that I spent a lot of time waiting for Andreja to walk to and from my ship and the various steps of her quest at a really casual pace in order to complete her loyalty mission. Fortunately I was able to complete it and didn't get soft locked at all, and once every step had been completed I was able to get her to follow me normally again.
Tl;dr; Don't talk to Delta while you have a companion locked in due to story or side quest reasons.