This is no glitch. There are several places in the wasteland where you can find the comet flowers. If you pick one up, it just grows again after a certain period/progress in the game and can be picked up again.
The one at the Ghost hideout is on the right about 10 meters away from the bridge when looking at the ghost hideout entrance on the ground next to the path.
If it has been picked up or hasn't grown yet, the plant looks like a cactus. If you don't see any comet flower there, just progress in the game and get back later.