It has to do with the "fix" they did to not make him able to jump through high projectiles with his arrow drawn.
He originally had this problem in Injustice 1, then (it is my speculation that) they fixed it by just making highs wiff on his krouch shot animation, but they didn't change the hurtbox of the character itself. It's probably a limitation of the way they use their models.
Anyway, since they changed it back, I think some of those Injustice 1 issues are kreeping back in. It's not exactly changed back, because in Injustice 1, he got hit from practically all highs, but it's probably kloser to the original Injustice 1 form.
@colt
I don't like to tag you, because I feel like people komplain too much to you, but I thought you should know this, if you don't already. Also, it'd be nice to know how right or wrong my speculation is.