Green shield drain is purged by hazard emitters. So is the plasma fire damage over time.
Heavy plasma torp isn't supposed to be survived, you're supposed to shoot it down. If you don't want to waste your time targeting them save a cannon scatter volley, torp spread, or beam fire at will for them.
Those things aren't bugs, they're challenges the map gives you.
Only thing I've noticed that seems like a bug in ISE is that the gates/transformers sometimes don't heal. Though every time this happens I'm the only one who notices or acknowledges it even when I post a message in the chat, so I wonder if it's a local glitch with my client or if they're actually not healing. Never have been able to destroy the gate before the other four finish.
Beyond that, sadly the shield neutralizer and HY torps are indeed working as intended. The invisitorps can usually be survived if you carry at least two Monotaniums and keep your shields up; evasive away and keep Hazards ready and you should be fine, though the invisibility is still an irritating, longstanding, unlikely to ever be fixed glitch.