Always been a glitch in GalCiv where if you send a ship on a long voyage where the shortest path to the ships destination it might go through out of range territory.

Usually happens when to keep the ship "in range" would cause it to take say 35 hexes to get there instead of 15.

Would not know as I stopped auto exploring in games after the first time I played Civ 2 and the unit headed of to nowhere I think it wanted to die heroically against a Barbarian.

Rule I have had since then " Never ever, ever auto explore". 

Then I like my surroundings explored systematically not in some chaotic random mess.  

Can't stop the ship now.  I had set it to manually move back into my territory.  If I try to stop that movement by right clicking on the ship it won't allow me to do that .  The message is "The destination is outside the ships range.".