Bone constraints not applied correctly I have a cube which is not rotated. And I have a bone that I want to add a copy rotation constraints where the target will be the cube. The problem is that when I add this constraint the bone is rotated in a wrong direction, as normally it should point to the x-direction but when I I make the copy rotation it points to the y-direction. If anyone could please advise why this is happening. I added screenshots below.

Before copy rotation



Cube properties showing there is no rotation



after copy rotation



copy rotation constraint



Edit:

After applying rotation -90 in x-direction the axis was good in edit mode, but once switching to pose mode the axis is wrong

After applying -90 in x-direction in edit mode:


After applying -90 in x-direction in pose mode:



And this is after adding the copy rotation constraint:
This behavior is normal. The copy rotation in world space will align the rotation axis of the bone with the cube (X with X, Y with Y, Z with Z). If you don't want the bone to rotate 90deg when you add the copy rotation you will have to rotate the bone in edit mode, making sure it aligns with the rotation of the cube (in your example, in edit mode, rotate the bone -90deg in X axis). 

The rotation in edit mode has an impact on how the bone is oriented in pose mode (in pose mode the Y axis of the bone is the one going from the head to the tail of the bone).

Then when you add your constraint to the bone, it shouldn't rotate.

Hopes this makes sens.