has any GM run this stunt against the players?

Once, yes. Players got trapped in a warp eddy for a while, wound up encountering a mirrored version of their own flagship. It was pretty hilarious for me; they'd built their ship to be an absolute deathcage in hit-and-runs, and I got some rather dirty looks before someone thought to scan the ship and realised it matched up with their configuration. Then attempting some shenanigans with teleportation since 'We know exactly where to teleport since it's OUR ship!', more glares until they realised how literally I meant it when I'd described it as a MIRROR of their own ship, and eventually they destroyed it, utilising the other vessel's warp core to create a shockwave that blasted them out of the dead area of the warp. Fun times!

I like it. I really need to remember that one

Sure - the players still managed to stomp the much larger enemy anyway, and pursued it back to its homeworld as it fled, which led me to have to invent the entire Second Logician War story arc the group will be going into.

*sigh*

I'm going to have to try this some day.