Thank you for the report! Hmm. You don't happen to have a save where this is reproducible, do you? I'm having a hard time thinking of a way this could happen, so assuming you didn't somehow miss them, this would be a particularly odd bug.
To explain a bit how it works behind the scenes: the game tracks these sorts of fleets in an abstracted way behind the scenes, and they come into being when the player is close enough to where the fleets would be at that time, whether at a starting or ending point, or somewhere along the way.
So, for example, if they're launching from Samarra, and you're nearby, the fleets will exist in-game. And since you saw them, that part of it looks like it triggered. At that point, they're in existence and would work normally, unless/until you move fairly far away in hyperspace-distance *and* at least a month passes, at which point they go back to "existing behind the scenes". But even then they would not be able to magically pass through an area in which you're waiting for them without "coming into existence" again. And if you were near the Samarra system the entire time, this wouldn't happen anyway, they'd just fly around following the same exact rules that you do.
So, right, this happening doesn't make sense - I'll keep an eye out for it! And, again, if you've got a save where this is reproducible, I'd love to take a look.