Couple things:
Doctor isn’t the traitor, Voss is. Laez line is confusing though. I think the idea is that the device was sabotaged to save you, but it also could be tadpole defending itself - I don’t know, it’s a bit of the mess. Either way Laez still believes in Gith so her priority is to report to captain things she discovered.
I reported the conversation with the captain for the very same reason. From what I understand, she sees your party as mercs she hired to help in looking for the artefact - you can admit you have it, or that you are still looking for it. However, once the traitor option appears, the game treats it as if you admitted to having the artifact.
The crèche has a very particular way of story progression, and it doesn’t seem to work well with variables.
