Although the documentation doesn't say so, I would guess that the Jacobian cannot be taken with respect to a symbolic expression like F/V. It has to be with respect to a named variable. So, replace F/V with its own variable like below,
syms CA CB Fv CAi k1 k2 k3
f1 = (Fv)*(CAi-CA)-k1*CA-k3*CA^2;
f2 = -(Fv)*CB + k1*CA - k2*CB;
A = jacobian([f1; f2], [CA CB]);
B = jacobian([f1; f2], [Fv CAi])
Best Answer