TM 40 (Aerial Ace) is in the game twice

TM 40 is the prize for beating the third gym, but it is also found in Kelper City near the Pika Taxi. Since TMs are infinite use, it doesn't seem to make sense that a TM that you are given as part of a mandatory plot event, and indeed still have, is lying around in some town as well. your bag doesn't even recognize that you have 2 of them.