It appears that wingmen don't always follow the player during a not-quite map change. By this I mean those times in missions where the player ostensibly moves to a different map, but in-game it's actually just the same map split up into multiple parts.
A good example is during Vorgon Conclusions, where the planet where we rescue Kal Dano is actually the same map as the following part with the Enterprise and Tholians.
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I've just noticed the same issue with some of the Fed Klingon War Episodes.
For reference, I am flying the Dreadnaught Cruiser.
Targetting one or other will also show them as being 100km or more away and nothing can be done to get them back apart from dying. Jumping out and back in might work but only if there's a respawn point.