Note: I'm unsure of the specifics, I just know that it happens.
Ships docking to an other ship will occasionally cause all its docked entity markers to to be visible for a split second (if you had "docked" and "turrets" turned off in the nav filters). This is especially noticeable when you recall a large drone swarm to a carrier: The nav icons will constantly flicker on/off, despite the fact that they were turned off in nav.
I noticed that this happens when drones redock to a ship via pickup points. I have no idea if the same occurs with normal contact docking. In my situation there were mutliple drones docking to different pickup points pretty much at the same time (or in really close intervals).
How to recreate:
1) Make a mothership with mutliple pickup points with drones/ships assigned to them.
2) Turn off "docked" and "turret" nav icons.
3) Recall fleet.
4) Watch as the docked entity and turret icons on the ship turn on/off
Note: I'm unsure if this only occurs when you're in the Mothership, and if it's visible to people in other ships. However, I'm pretty sure that the entity flash occured even when I wasn't in the mothership (needs testing).