That's just how it's supposed to be.
When you beat Geovanni you should get a Silph Scope which can see through a ghost's discuise and show what it really is.
Next, go to the Pokemon Tower in Lavender Town and climb up all the stairs. On the stairs going to the top floor a Marowak will appear. This is acctualy a ghost but the Silph Scope shows you it's just a dead Pokemon. You must kill this Pokemon or just use a Poke Toy to carry on. (Trying to catch it doesn't work!)
On the top floor you will see some Rocket members. Beat these three to rescue Mr. Fuji and he will reward you with the Poke Flute which can wake any sleeping Pokemon!
Don't worry about Team Rocket being in Celadon City, it's supposed to be like that. :)