Any transit generates an immediate interrupt and should end movement for the transiting fleet in that increment, so you should get a detection following the transit and see the NPR before the next turn.
If that isn't happening, its a bug.
Does the interrupt happen at the end of the sub-pulse during which the transit took place? I'm fairly sure the movement for transitting fleet doesn't end unless they require a standing order (or the AI equivalent of such) to proceed, I've observed ships stay at the jump point as long as I keep advancing time in sub-3 hour increments, losing contact the moment I advance enough for my own standing orders to kick in, and I've seen transitting ships instantly register as lost contacts, though direction of their movement could be discerned (
example, those at the jump point were usually case 1, some of those away from it were case 2).
Then again, my suspicions about entirely undetected transits could be half-wrong because some of my jump points only have detection on one side, so I guess a transit through a jump point with a buoy on the entry side would potentially not generate an interrupt under the current system, as there's no detection on the exit side?