According to CheeseLover, the following missions are not replayable from the Replay Menu:

Paparazzo The Partnership Grass Roots - Franklin Grass Roots The Smoke-In Seeking the Truth Accepting the Truth Assuming the Truth Bearing the truth Exercising the Truth Special Bonds Death at Sea What Lies Beneath Nigel and Mrs Thornhill Extra Commission Far out The final Frontier Mrs Phillips Damaged Goods

I suggest they get removed from the Individual Levels leaderboard.