In the maps themselves, the activation of the Sewer system turns on an in-game switch that changes the teleporter so the player ends up in an identical room with sewage water that can be cleansed with Seed Flare. However, because the two rooms are made on the same map and the distance of "Black" or blank spaces isn't enough, you can see both "rooms" at the same time. Just adding more black spaces between the two should solve the problem, and subtly changing the teleporter destination.
Also, I'm unsure if this was intended, but for Harmony's Gym, there is an old woman cleaning up trash outside of Route 10. It seems that it's a plot device preventing the player from moving onto the next city and route before beating the local Gym. However, there's only 1 piece of trash blocking the exit instead of 2, making it so beating Harmony's Gym isn't necessary to move on.