In The Flash season 1 episode 11 Hartley Rathaway says he knows Wells’ secret (about him being The Reverse Flash):
Barry: Looks like you're not as smart as everyone says.
Hartley Rathaway: Smart enough to have figured out who Harrison Wells really is. You see, I know his secret.
That was for you, Flash. Feels good to have the great Harrison Wells behind you, doesn't it? But one day, this man will turn on you... [laughs] In a flash... And even you won't see it coming. I only hope that he leaves you in better shape than he left me. If you're lucky, you'll only be dead.
[laughs] I almost forgot... I told your pet I know your deep, dark secret, Harrison. Have fun letting him in on that one.
He even saw Wells on the floor with his legs vibrating.
Hartley Rathaway:Tell me, Harrison. Am I still you guy?
I’m confused. How did Hartley Rathaway know about Wells being The Reverse Flash?