there have been questions as to whether wearing MotTM may lead to Crota "seeing" a hunter even after the hunter has gone stealth after a melee strike. may just be glitches, but perhaps not?
MotTM is not related.
A few things can cause it, mainly Scrota storing his aggro from before he kneels and then smacking the f out of you once he stands. The aggro is generated from non-invis form so it doesn't matter if you are invis from blink strike afterwards. This is why the killed-while-invis is associated with the blink strike, totally unrelated to armor. Also why he won't smack you while invisible the first time you jump up there regardless of your armor (either super invis or crouch invis typically).
E.g. Attacking w sword before the first shield break causes your invis to go away and can result in Scrota aggro that lasts until after he stands again. It's happened to me many many times even though Don't Touch Me is my standard sword running exotic.
This was also an issue with the cheese patch which seemed to complicate the storage of information related to a shield break and the corresponding immune shield. Shield break is generated "locally" but immune shield timing is cloud-based/Bungie side or w/e the technical description would be. They wanted to prevent host Ethernet disconnection from stopping his subsequent immune+stand response but it just added fuel to this dumpster fire boss fight.
So Scrota might not start kneeling until his immune shield is already active if lag is bad for the sword runner which can further throw off his intended response to blink strike invis. It can also mess up what the sword guy sees as Scrota's shield break timing, like yesterday doing HM Scrota: on my screen I saw DeathJR sword slice before the first shield break. It resulted in him getting smacked when Scrota stood even though he was clearly invisible. But on Ruthless DJ's screen Scrota was already kneeling before he attacked.
This now concludes another episode of "Dr. Boguester Yells at Clouds."