Hmmm... I did have to fiddle around a little to make sure I was getting things to click into place, otherwise I found that it was very easy to end up with bits not quite fitting right, and feel like things are really not lining up. I didn't use the instructions (which is usual for me, and probably for most people?), but they might help clarify things.
I think the hammer handles are actually quite logical and realistic... a Warhammer (or similar large weapon) can really only be carried near the head (or you'd drag it along the ground), whereas when swinging it you'd have one hand near the end of the handle and another closer to the head.
What is annoying, of course, is that the thickness of the actual handle means that Hasbro had to make artificial handles protrude out to facilitate the standard 5mm grips. These are not pretty, but the compromise would've been to make a too thin handle, or make non-standard grip size for Magnus's hands.