Not actually a bug, although I plan to change this behavior at some point.
Right now, the way the scouting works is this:
1. Each system has a "last scouted second."
2. Each ship has an "existing since game second" property.
3. The intel summary shows you counts of all the ships at each scouted planet that have existed since at least before your last scouted second at that second.
4. Therefore if ships die, you know this, and if ships enter and leave the systems (specops ships), then you also know this to a certain degree (if they existed since before you scouted, then you know this).
Later I need to make it take more static snapshots that only get updated when scouts are present. Of course, the downside of that is that then when ships die and your scout is not present, the intel summary will still say there is some ungodly number of ships there. I'm not certain which behavior I prefer at present, so hence I've left it alone for now, though it is on my list somewhere...
