I know exactly what you describe.
Happened to me during Gamma and beta phase last year.
Ticketed it and never received an answer.
Didn't happen since release so i thought it was fixed.
I think i even read something about it in a long changelog.
What can you do?
Try it out with a sidey, maybe it happens just with a special ship.
Ticket it (haha sorry)
Don't use this station anymore.