I was inflicted with a disease when i was turned into a werewolf which removed the disease flag and made me 100% resistant.
but when i was around town people still tell me I do not look like i am feeling well and when I go to the shop that shop keeper tells me that i may have so and so disease that they may have a cure for such and such even though i am no affected by anything

If you're talking about the alchemist in Whiterun I'm pretty sure she says that to everybody. She's said it to all my characters even ones who don't have diseases, and right after she says "I think I have something for it, it's quite common in Cyrodiil." I think it's just something they put in the game to give the store a more realistic feel, like she's actually trying to get you to buy her potions. As for other npcs, idk why they would be saying you look sick unless it's a glitch.

okay i visited a shrine that removed disease and blessed me and it removed everyone telling me that i am sick so it seems it is a bug that happened that is easily fixed by just visiting a shrine