Only one that I've found so far but it's a big one. I'll refrain from publicly saying which enemy.
But what you should look for is loot that drops in response to an enemy being gone rather than a standard death loot table.
It only happens when all other objectives are complete first.
I also suspect it might prematurely trigger new waves in things like No Win Scenario.
This happens when using the two piece set bonus Temporal Backstep. Using it doesn't trigger a death but it can cause a mission to think an enemy is gone.
I'd also like to see what if any impact it has in missions like Coliseum where you get tractored... and I'm also looking at testing it in combination with other ship effects like Transwarps, queues, and autowarping out of a map. (Ie. if two things are going on at the same time.) Also what happens when you use it on destructibles or in special cases like Night of the Comet, when near comet chunks.
In particular, what I think is relevant is that it's causing some part of the game logic to register you and your enemies as "not there." In the Foundry, my experience is that if something flags off a completion or interact with an object and that object is somehow otherwise removed then the completion flag triggers. (Interestingly enough, I can think of some test scenarios where a Foundry mission could have some different results for anyone in a two console timeship. You could have a mission whose progress changes as a result of Temporal Backstop. I could build a mission DESIGNED to do that.)
Might also be interesting to see what happens when two people manage to use it simultaneously in PvP.
We're aware of this situation and are investigating solutions.
Off the top of my head, it probably means either reworking some specific mission logic or making a list of things that have to be made immune to the freezing effect. Making certain things immune would be the easier route but would probably mean missing some things. Reworking mission logic means getting the chance to possibly add polish and remaster some content while you're in there.
You could do a crazy reworking of the engine itself if you plan to have more similar effects in the future. The downside is it would take longer and break Foundry missions, which tend to exploit wonky logic. (My first one on Holodeck "Currents Turned Awry" exploits how making an object vanish triggers it as a component complete.)
Beyond that, the best solution might be a radical overhaul of the set bonus, something I imagine PvPers would welcome, depending on how you did it.
For example, maybe instead of having the 3 piece enhance Temporal Backstep, maybe give it the ability to launch mission replay directly from the bridge without travel. (Or --- and this wonky -- the ability to select your past and future self as away team members. Just a souped up version of security/redshirt that are an alternative to BOs. Only these are costumed to look like you and given better default weapons/abilities.)
I really dig the mission replay approach because it could make that bridge a nice hub for friends gathering to do mission replays together.