The error message is fairly clear. You're comparing two matrices of different size with == (also called eq). == only works with matrices of the same size and also return a matrix of the same size which tells you which elements are equal.
Possibly, you should have used isequal instead. This will return false if the matrices are different size or if any of the elements differ and return true only when the two matrices have exactly all the same elements.
if isequal(gen_gate(end,1:2^n),f)
