Aurora is not interrupting properly when an NPR transits into a system whose WP is under observation by active sensors.
I've had a picket watching the WP into an NPR home system, about 1M km off with active sensors with a range of about 12M km. The NPR had already sent through an gate construction ship (based on size and behavior). I just did a 140,000 second update (which resolves to 40 hours), and got a interrupt enumerating 3 new thermal contacts at t+8 hours. When I went to look, the NPR had sent 3 ships through the WP, but they had already moved out of range of my actives - about 15M km. Fortunately, I had just saved, so I reloaded the DB and ran the same update with 30 second timestep (yeah for the rewrite - it didn't take long at all). This time it worked ok - they were detected at 6 hours, 31 minutes (note that they were already off the WP, but I'm willing to chalk that up to "activation lag" by bored picket sensor operators).
I am stepping through the code to try and figure out what happened. The code is set to generate an interrupt if a transit is actively detected by a hostile race or if the transiting ship is only picked up on passive sensors and its identity is unknown. I am guessing this was a neutral ship, in which case I probably need to adjust the logic so that time also stops for neutral NPRs but perhaps not neutral player races. Or perhaps just for recently discovered neutral NPRs. Before I shoot off in this direction, could you confirm if the NPR was neutral or hostile?
Yes, it was a neutral NPR.
From my experience later in the game (where they had commercial ships in my home system, and were interrupting every few hours of game time), I'm not convince that throwing more interrupts in is a good thing. I think this is a very difficult problem for you to solve, since what is needed is the ability for Aurora to read the mind of the player as to what's an "important" contact that needs an interrupt and what's noise. This is especially difficult since exactly the same event (detecting a transit) can vary in importance according to the current situtation. I've had the following thoughts about it:
1) I think there has to be a way for a player to select (on a race-by-race and/or system-by-system) whether or not he wants an interrupt to be thrown by a "harmless" (non-hostile) event. I suspect the easiest way to do this is to put a "trusted" flag into diplomatic relations, which can be toggled. If a race is trusted, only hostile acts (e.g. missile launch) should cause an interrupt. There might be levels of trust too, e.g. trust commercial ships but not military, although I'm not convinced there's much added benefit from this extra complexity. One way to think of this is as rules-of-engagement - the rules for a trusted race would be "don't interfere, but report their actions", with the processing of the report happening at the end of the update.
2) I think that NPRs have to be inclined towards trusting others

In particular, they should trust any race for whom they're carrying cargo - otherwise you run into the situation I had with my home system. You might need to cheat a little here, and have the interrupt decision code "peek" at the detected fleet's orders to see if there's hostile intent - if there is then an interrupt happens and the NPR can change its behavior.
3) One thing I'd like to see is a "contact acquired" to "contact lost" line on the screen (similar to the movement tails) for contacts which didn't cause an interrupt but made it out of sensor range before being lost. This comes back to the RoE "observe and report" idea - you get the event notification at the end of the update (as it is now), but you also get a visual cue as to where the contact was headed so you can go look for it if it's going in an unexpected direction. If I'd had this, it wouldn't have been a big deal that I didn't interrupt when the aliens transitted, since I'd know where they were going.
4) Just remembered this one while typing the last bit - it would be nice to have a "Move in direction xxx" order, as opposed to "move to a waypoint". Then you could send ships searching along a bearing towards a lost contact, rather than having to set up a waypoint.
John