I think once was when Shiro was transfering mana to her after the berserk fight. In the anime , they changed that scene as Shiro being on top of her and Tohsaka removed Saber's ribbon from her neck. It was actually a 3some scene.

And 2nd time was before the final battlel.

He is the Servant of one of the series' main heroine, Rin Tōsaka. Due to an incomplete summon, he apparently has no memory of his previous life or identity. Archer is sarcastic and cynical - but under his hardened exterior lies a complex and dark personality that unfolds throughout the story. Though skilled with ranged weapons, he can hold his own in mêlée combat. Archer considers Shirō Emiya's idealism to be weak and delusional, recognizing Shirō's mentality of "wanting to save everyone" as naïve and impossible.

From wiki.

He only realised later on who shirou really is.