I found that 90%+ of those bugs can be avoided by killing adds asap and ignoring HK till they are gone. Haven't had any of those bugs since my groups started doing that, you take a bit more damage (more strain on the healer) but its not bad and def. worth it.
The wipe chase bug I kinda like, let him come while you regroup and finish him without him resetting his hp
Yep if your doing Foundry and group is full columi or better your going to over dps him and its going to bug out (been this way since release sadly).
Methods to prevent it.
Leave 1 DPS off boss 100% of fight (add duty only)
DPS adds down first once they spawn
Never DPS HK outside of center chamber spawn point (ie when he vanishes and appears on the side, just wait - kill adds etc dont touch him let him vanish back in and wait for consoles).
If it does bug (usually you don't get the consoles to smash) immediately whole group run to open archway(doorway) which pulls HK out and over there. Burn him down and carry on.
Sorry to say I gave up on Bioware fixing this encounter months ago, so when I do have to run it, we make do with what works to prevent the issue.