First off, chemical kinetics is macroscopic. You don't apply the equations to a container with two molecules.
Second, it's not that surprising. Suppose we have a container with enough molecules for kinetics to be meaningful. For your first reaction, supposing it is an elementary reaction, we can safely say r=k[A]^2 and for the second, again assuming elementary reactions, r=k[ B][C].
You would not suspect the rates to be the same given the same concentrations. In the first case, A is reacting with itself to form some other molecule - the key is that every molecule in the container is A. It doesn't need to worry about bumping into the wrong molecule.
In the second case, B and C react but B and C have to waste a lot of time bumping into the wrong partner before they meet eachother and react.
The problem here is viewing it as two single molecules hitting each other. If its just two molecules, then of course the rates could be the same but those rates =/= k [A]^2 and k[ B][C], respectively.
Also, not all rates of the form r=[A][ B] are elementary and there are built in approximations and such. You know the distinction between a composite and elementary reaction, yes?