
Since compass is only trusted to Cain and only he should have it, it was a secret that he ever gave it to Sid. Doctor understood that Sid had ulterior motives(since in their conversation Cain made clear he needed Doctor alive), so by saying "is it that you no longer had the compass?" He hinted to Cain that if he(doctor) knew about Cain currently not having compass, that meant that he saw someone use it, but compass was only supposed to be used to find doctor himself, so doctor being dead was a lie and “Sid” was the one who killed him(exempted at least).
Well the fact that doctor understood someone was using compass was because he was basically untraceable and compass would be only thing he would be found so easily with.
Idk if it helped, I hope it didn’t make u even more confused
there's still some stuff i don't fully understand hhh
remember that revelation part where the doctor is trying his hardest to reason out and gain cain's trust in front of sid?? how did he know,, or rather, how did the doctor came up with an answer, "is it that you no longer had the compass?" that made both sid and cain flinch?? what was his motive behind it? is he trying to force sid to confess and corner him? i'm pretty sure he was still confused on that part, since he couldn't confirm to himself whether or not sid was the mastermind of the attack;; so how..??