Just looking over the campaign (I don't know how far you are, but it's got to be pretty far if you met the Shepseskaf)
mission 0: no warpouts at all so no problem here
mission 1: no warpouts
mission 2: the Cho, Cardinal, Idomeneus and Regensburg are all present at mission start and warp out after a full charge cycle. Some Ares jump in and out, they're fighters. Serkr Team (a group of next-gen shock jump corvettes) jumps in, takes a little while under risky attack to charge up, and jumps out. No problems here
mission 3: The Meridian is present at mission start and can (obviously) warp out. Same goes for her escorts. I think the only potential for a real problem here involves the
Yangtze, which might be allowed to jump out very soon after jumping in depending on how the mission script plays out...but most players will probably never even see her, so I'm not sure.
mission 4: obviously no warpouts
mission 5: no capship warpouts
mission 6: the Redoubtable is present at mission start and warps out on a full charge. The AWACS can jump out really soon after jumping in, but they're very small craft. The Valerie doesn't have a chance to jump out after jumping in, nor does the Indus. The Atreus is a next-gen combatant with a sprint drive. No problems here.
mission 7: no capship warpouts
mission 8: no capship warpouts
mission 9: This one I'd question why the GTVA didn't jump one of its warships clear. Presumably they were unwilling to risk abandoning the Agincourt, though it's pretty negligent that they didn't manage to get even one jump-capable ship off the deck - the warships themselves were probably still in charge cycle after their last jump. No capship warpouts, however, except the Agincourt if you fail the mission - it takes quite a while to charge up. I'm less happy with this one but I don't think it has glaring issues.
mission 10: the Indus and Yangtze won't try to warp out at mission end, presumably because it's a situation just too critical to abandon the fight. Torpedo Two jumps in and gets shot to **** before they have any chance to jump out, unless you're really good. The Hood jumps out at the end of a full charge cycle. The Medea jumps in and doesn't get a chance to recharge before being shot up. Seems fine.
mission 11: the one I'd worry about here is the Hesperia, but I'm not sure exactly if or when it jumps out - it might be a bit quick. Possibly a problem here, but it's not tactically relevant.
mission 12: nuttin big
mission 13: the Spectre is an AWACS and has time to charge anyway; the Shepseskaf has something seemingly akin to a sprint drive setup, which makes sense given how excellent Vasudan reactor design has always been. No big problems.
mission 14: jump dynamics are obviously a big deal here, but the Antenor and Norfolk both get caught on the down end of a charge cycle, and the Carthage has to use her sprint drive to escape. Seems to play by the rules.
mission 15: none of the UEF ships that jump in are able to charge up and jump out, except the Indus, which is the first to arrive and which gets to spend a large chunk of the battle in the relatively safe back rank. It doesn't have a nav fix ready either. A large number of GTVA ships are able to warp out, but they all had time to charge up. Seems fine. Mister Cuddles might break the rules of course
mission 16: heh.
All in all the rules seem pretty consistent. The one I'd worry the most about is the Hesperia...checking its departure cue, though, it doesn't have one, so no problem there! After that the biggest problem is the Yangtze in Post Meridian, which can, if the mission proceeds along a certain route, jump out immediately after it jumps in. That's a clear continuity error, but it's unlikely to happen.
This is the same kind of check we ran through multiple times during development.