Locked file that I can't remove
I managed to figure out the problem.

First I used ls -laO which showed the flags for all files. It turns out that both schg and uchg had been set on the files. To override those, I did:

sudo chflags nouchg /Applications/Karabiner-Elements.app
sudo chflags noschg /Applications/Karabiner-Elements.app


This unlocked both flags, and allowed me to delete the files.

Thank you all for your help.