Sometimes there are some animes that is so confusing, you can't understand what the heck you just saw. Sometimes storyline doesn't make sense, sometimes some details are never explained, etc. Some of these animes mess up your brains for quite long time. Let's talk about those animes.
Confusing animes for me were:
Neon Genesis Evangelion
I couldn't understand the ending. 26th episode seemed like Shinji got over his mental dilemma but that didn't give a clue about what happened outside. End of Evangelion was just so confusing, I wasn't sure if I was watching the right thing. And what did that mean by Shinji chocking Asuka at the end? It was just confusing.
AIR
It was quite confusing since the part where Yukito becomes a black bird. What happened to him? And what happened to Misuzu at the end? Did she die or not? I didn't understand it. (plus, it was very depressing)
Bobobo-bo-bo-bobo
Honestly, I only saw bits and pieces of this and that episodes. But I was always confused by this anime. It seems like it has no plot but this was too beyond making sense. I never understood why there was a guy inside Bobobo's head or why the characters are wandering or anything. Maybe it's because I never sat down to watch in order but I don't think it will make sense even if I did that.
Higurashi no Naku Koro ni
I kinda understand it now but it is still a little confusing. I could never tell about Mion/Shion until I watched the second season. I was never sure about what the heck is "Oyashiro-sama." So many actions characters did, like Rika stabbing herself on her head (I mean, why did she do THAT?), didn't make a lot of sense.