On some commemoratives and nearly all medals, the alignment is the opposite. If you turn a medal over from top to bottom, the reverse will be upside down, because "medal alignment" requires that the coin reverse be right-side up when the coin is turned from side to side (rather than from top to bottom.) The reason for medal alignment being different is that medals are frequently hung on ribbons or chains, and if the medal gets turned over, the wearer wouldn't want his medal to look upside down.
All U.S. coins, and nearly all world coins, are struck in one or the other of these proper die alignments. Die rotation errors are known to exist, where the coin's reverse isn't precisely lined up with the obverse. Several State Quarter types have been found with die rotations ranging from a few degrees off, to a full 180 degrees off!