I really don't think so, but it sounds like as good a guess as any. I do not let my survey ships travel that freely. If the same might be true for colony ships, then perhaps that is what is happening, but, let's face it, such a message for such an occurrence, regardless of the ship class, goes beyond confusing. Worse, I had no indication what so ever of the location of the problem, or the name of the ship involved, hence, no clue what so ever to help me figure out what to do about what ever the problem may have been.
Just in case anyone is wondering, I am calling this a BUG, hence my reporting it via a ticket.
I am also guessing that any ship involved in this problem would have stopped moving and I would have seen it when I went through the inactive ships during my next turn. I did see a colony ship that was inactive, but was a long ways from its previously assigned target destination (a planet which had become colonized by another civ).