Did you have any units capable of attacking them within range? I've seen units move through occupied territory before, most specifically allied units through the soviet union in the cold war while trying to get to Vietnam. Despite no transit treaties, they'd continue attempting to move through Russian territory, being destroyed in the process. I wonder if you had units in range to attack them, because I suspect they would have.
One ground unit was at Istanbul and there were two Patrol types within the Strait area - neither attacked.
Yes, I saw this also saw you type case in SR-49 Cold War.
Another similar issue was the Suez Canal during SR-49, in which Egyptian land units attacked French aircraft onboard French carrier attempting to transit the Suez Canal. The attack were only against the aircraft onboard, as if they were "flying" - weird. No attack or impact on the carriers transiting. Neither country was at war either.
Don't know if that was ever fixed.