I opened another project then went back to it and now they align fine inside, don't know what happened but fixed now.
It was weird because it happened to all my atlases and anything I added in NGUI, but now they all are fixed after I did that.
Edit: Stuff I put inside a UI panel and Scroll view forces clipping to "Constrain But Don't Clip" which also adds a little gap.
Edit 2: As I was working suddently everything jumped back to how it was, now there is a gap like showed in the first picture again.