Unlike the normal aircraft in the Aircrafts mod, which are typed as "cars", the aircraft in Lex's mod are typed as spidertrons to enable them to move more intuitively with WASD (W goes north, rather than whatever direction is currently "forward" for the vehicle).
This means that these aircraft will be moved into the factory if they fly over the entrance, the this mod sees them as spidertrons. This can be disorienting enough on its own, but Lex's also uses stickers to control the aircraft speed rather than setting that speed via the leg prototypes. These stickers do not appear to be re-applied when the aircraft is transported into or out of the factory, and are only re-applied of the aircraft is "mined" and then re-placed in the world.
Recommended fix is either to figure out how to retain the stickers (I couldn't figure out how to do it, but I only sorta understand stickers in the first place), or simply exclude Lex's aircraft from the teleport. I attempted to do this by adding a conditional that looks for any spidertron that starts with "lex-flying-", but I couldn't get it to work. If you can figure out the sticker re-application (or perhaps even if you can't), it might be easier to make this a setting, either specifically for Lex's, or simply having a textbox "spidertron blacklist" which can take entity names to exclude from the teleport. I ask this mostly because I almost never want one of my Lex aircraft to enter a factory, but I do use that feature heavily with other spidertron-type vehicles, including the Space Spidertron (the other mod that I'm aware of that adds a "flying" spidertron, and incidentally doesn't have this issue because it doesn't control speed via stickers).
