Had this happen to me as well, several times in fact, and what really makes it worse is that it's a time sensitive mission. Once I even had a ship spawn with no Tholians guarding it. (Not really complaining about that one..lol )
This seems to be happening more and more, as has been pointed out, its a bit disastruos in a time sensitive mission.
The other problem I encounter is the invisible hostage ships, which cant be be rescued (the tractor beams are visible, but no ship), which means that spawn is locked for the whole round.