They did miss one info. Sparrow's error, I believe everyone knows so I won't explain anything here.
What evidence you mean?
Well, if you say Roxas could use Kingdom Key even when Sora's using it in CoM, then that's a contradiction. How could there be two Kingdom Keys at once? My thought is, they had never thought of using Roxas. He was a, somewhat, a backup. Their original plan is to have Sora, the Keyblade Wielder at their side (I think there's actually proof about this, I just forgotten where). And if you have the real thing, why on earth do you want the fake? However, when they failed to control Sora, their plans were disrupted. However, since Roxas could use the Kingdom Key after Sora went to sleep (Which means I thnk you're wrong), they decide that his Nobody would do.
To answer about your question that Roxas is in the Organization before or in CoM, I think they gave him a weapon (Most likely a sword) to fight at first, when there was no Keyblade he could wield. After CoM, Roxas suddenly could use the Kingdom Key. This actually suits KH style, and it sounded logical. Think! Does all the Organization members used their former's weapon? No, they just use the same kind of weapon, not necessary that weapon.