I've been having a lot of crashing in Zeta Base, when I have not had it before. When checking any of the security camera screens (mostly the ones that just say EVACUATE or show a picture of one of the aliens, but also the ones that show doors too), I get a crash to desktop. I'd say about 2/3 of the time it happens, pretty reliably. To be fair though, I just click on EDuke32_64bit.exe and reload a save and I'm right back in the game, so it's more of a nuisance (though I can see other people getting really frustrated by it). I do not remember having this issue in the previous build I played (Episode 2, with the v2.0.1 patch and the Megabase medical research patch), only the current build. And just in case, I did indeed uninstall Megaton Edition.
In addition, a minor bug was that any time I returned to Zeta Base Lower after visiting Upper or Bio-Labs, all the sound is permanently lower pitched, as if wearing the enviro suit. I even went back to the beginning and put the suit on and off again, sound stayed like that (but only in Lower; the other two maps had correct sound).
I don't know if it matters or helps to try to reproduce it but I was playing as Geoffry, with all his default weapons (though fully upgraded at DeeperThought's desk in the base), and the special equipment I took into the level were the spirit shawl and some torpedoes for the dart gun, I don't remember bringing anything else.
...also I just want to share/brag, I found what I hope is all the secrets in Zeta Base. Took me two days.