This is not an uncommon situation. It is not due to a bad design it is usually due to the HB being put on by a mechanic ignorant of MB's. Unlike most HB's, the MB HB is pinned rather than keyed. Techs are accustomed to putting the HB in place on the keyway and then driving it in place with the bolt. That will wreck the crank on an MB, you have to put it in place and drive it down with the bolt, then REMOVE the bolt and ensure that the holes align, then put the pins in place. If they are not aligned, pull it and try again until you can tap the pins in place.

You have to put the HB in place slightly counterclockwise of where it needs to align, because the bolt will turn it some.

Hope this helps,