Before I list everything: posting gifs is garbage. Things like giphy integration degrade the signal-to-noise ratio, and I rage against it in every chat app I use. Even in off-topic rooms it'll random make following a conversation annoying at best.
Anyway, hipchat's faults:
Search is garbage.
Editing a message is garbage.
Joining a room/messaging a specific person on mobile is annoying.
I'm not sure about how Slack handles it, but when a person leaves our company, our Hipchat chat history completely disappears. All those decisions we made with our old Product Manager via private message? Into the ether.
Want to delete a file you uploaded? Too bad. Maybe you can do it via the web interface?
Want to delete a message? Same deal.