Are you sure the action is not rotated in the stock? Some stocks have large holes for the action screws that allow the action to be tipped left or right in the stock.

Even if the holes in the receiver are drilled incorrectly, I don't see how this will affect your point of impact.

Believe you might have an eye or scope issue.

If the holes in the receiver are drilled canted, the base/rings/scope is still attached to the rifle securely. There have been instances of scopes running out of adjustment before being able to zero the scope.