I've run the raid up to oryx teaching people the mechanics over a dozen times, plus I've beaten it 6 times, and never once has any of those things happened to me or anyone I played with, with the exception of number 3 but that's not a glitch, it's a mechanic of the fight. If you are not shooting oryx in the chest while your team is collecting the bombs then he will not be hurt by them. You don't need to do a certain amount of damage or use high dps weapons even, it's just about providing continuous damage to him during that entire phase.
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we do. trust me. I'm always running relic and sitting there hitting him with sniper while team detonates and then switching to my primary to keep continuous damage on him. this is a legitimate glitch where he just doesn't take damage and then immediately teleports to the middle and starts mortar round.
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Then the only explanation I have for that sort of thing happening to you is a great amount of lag. Make sure you are raiding with people in the same continent as you, that you are using a wired connection, and all that stuff.