The whole thing started with someone finding something wrong with the 'Curl' wrapper around a packet that's being sent from A->B. Apparently, this violates a EU-CMA security protocol, and this is an issue. Lots of holes in my knowledge there, but I got the jist.
What I don't get, is HOW this became a bipartisan issue with HN/Reddit. Because if you read the 124 pages, it becomes clear that both the IOTA team, as well as the MIT team were bad at communicating with each other, the purpose of this bad communication is unknown, but both are at fault.
So we at HN look at some emails from IOTA and call out their unprofessional behavior, and Reddit does the same thing with MIT's team.
What if someone has no perspective of how these communications usually take place? It looks like (upon the assumption that IOTA's team member was indeed in an 'incomprehensible' state when he typed that email out) MIT's team member without a second warning, just went ahead with publishing the paper.
So what's the big mess? It's pretty clear that both parties messed by being sloppy at emailing each other.