Are you sure they just weren't way up?

Positive, they were chasing something of the enemy that went out of the gravity well(may phase jumped or moved like his fleet moved), not sure what they were chasing tho...(Fun thing is, his enemy was vasari, maybe it's the TEC following the vasari in the lore )

I have had the same problem on my own made map(altho slightly different), where my scout would jump through a wormhole, then decide to go back to the other side of the wormhole by normal speed, not even phase jumping... luckily, its a small distance, but still an annoyance.