Task Force Hippocrates -- Beamed to USS Eagle. Klingons teleported randomly between various sections of the map. Several seemed to become stuck in the walls. Still able to finish mission.
Skirmish -- Boss Devidian at the end walked into a crate several times. While inside the crate, it was untargettable and immune to damage while still capable of shooting me. After many Revives, it eventually died.
What Lies Beneath -- Flashlight refused to stay turned ON for more than a few seconds at a time.
Night of the Comet -- Comet was not there. Exited/re-entered. Comet split into 2 pieces instead of 3. Exited/re-entered. Comet split into 3 pieces. No further splitting occured. Exited/re-entered. Comet split into 3 chunks. First chunk split into 3 pieces and the remaining 2 chunks immediately disappeared. Seems too heavily bugged to be completable.
The Ultimate Klingon -- None of the ships on the initial map did anything. They sat there and let me blow them up. One Vor'Cha took far less damage than the others. It took at least a full minute to be destroyed. After that, no issues occurred.
Nearly every map with corridors had teleporting NPCs. BOFFs were also very prone to getting stuck for no reason. They'd be following through an empty corridor and suddenly stop and were entirely non-responsive.
One of my BOFFs had the fire extinguisher equipped. She refused to use anything else. Just followed me around, constantly spraying the extinguisher. I have no idea if this is a new bug or even intended.
This ^^ 1,000 times THIS. I've experienced pretty much all the issues you mentioned since the last patch and more, but always it was glitched/bugged away team members and it dident seem to affect the mission npcs so badly I couldent finish the mission. But now on "The Gates of Gre'Thor" I complete the 1st mission objective and then after that nothing, there is no gatekeeper to protect, noone is doing anything, i'm alone on the dock praying something happens....and nothing. This sucks. I hope they fix whatever they broke with this dam "Let's spam lockboxes all over the place" patch. <sigh>
I don't know if it's intentional or not, but I had the same thing with the BOFF's using the fire extinguisher exclusively when equipped with it long before the most recent patch. I finally deleted it from my account because they couldn't play nice with it. I just started the Borg episode missions and I haven't needed it yet.
Don't forget Stranded in Space too. One away team member remains on my ship transporter and the others vanish as soon as I go through the first door. The first door for me doesn't open either I can walk right through it.
Tried playing Clipped Wing (USS Eagle) and I have the same issues regarding Klingon vanishing too.