They've never fully explained that, I've just taken to thinking that all the Angel's are probably just "cursed". It's probably just an innate thing that occurred after the humans fucked up the last time. The God of Owari no Seraph was like yo wtf and felt the need to wipe out the humans like he did Sika Madu's faction to avoid them committing taboo. He probably didn't wipe out the children of humanity either because they were too innocent or some other junk like that and felt that absolved of them of that sin.
But this probably lead to all the remaining angels being given an instinctual mission to eradicate all humans cause they fucked up.
It's not a confirmed thing, I've just always thought of it like that, so I've never questioned the narrative too much. I could be wrong but so far it's worked and fits mostly into the story.

I'm not super confused, and I pieced together what's happened but this is some wack ass shit. A plot twist like this is too funny I laughed my ass off when it happened. I'm not minding it too much and I don't think it'll effect the reading experience much either. Just an odd choice that's for sure.