Very good, that you find a potential reason for the mess of spaceflys!SirNukes wrote:...
In short, the fundamental problem is either bad documentation or bad behavior of the "create ship" command (depending on which angle you look at it). When a spacefly is requested, the script engine redirects from Create to CreateSwarm, so a whole flock of spaceflies are created and their scripts started. The documentation doesn't mention this, and modders do not expect this behavior.
... They destroy the single spacefly they meant to create, but not the unexpected extra swarm.
....
But maybe you can give us more details of the scripts and places of problematic code in this scripts/mods?
It sounds like, that the spaceflys are created as helper beacons in these cases - so alternatively to modify the create ship behavior in general, it may be another approach to modify the problematic code in these mods...