Steps to reproduce:
battle a wild Pokémon while the config setting "allowVanillaMobs" is true (or just spam a bunch of zombie spawn eggs beforehand)
win the battle at night (optional if you did the above parenthesis)
get swarmed by zombies while deciding whether or not to learn a move, let a Pokémon evolve, etc.?
????
Profit!

While dying may not be too much of a problem in and of itself (depending on settings like keepinventory and the presence of commands like /back), it does present a problem if one of your Pokémon was about to learn a move, evolve, or something else of that nature. Pretty sure, for instance, that my Arbok (which took long enough evolving from an Ekans for me to get killed) missed out on a move at the same time that I was discovering this. Fortunately, in this instance, I'm the server admin so I could just give myself a TM if it was enough of an inconvenience, but nonetheless this is probably not intended gameplay.
possibly (but not likely) related to #13099
probably not a duplicate of anything (I checked every report in the 150 search results for "player")

follow-up: looks like the move learning UI shows up again next time you start a battle (or at least it did for me), so that's good. Thanks for that much, at least, Pixelmon developers
of course, the underlying bug is still an issue, but silver linings, you know?

seems interrupted evolutions are not so lucky: my licktung's evo just got postponed until the next level under similar circumstances, even though the animation had started by the time I got killed... Don't know if this additional information is actually helpful or not, but I like to provide whatever I find out

There are currently no plans on changing this. It's just part of the risk of playing with mobs enabled.