Homomorphism with subtraction for Pedersen Commitment
You used the wrong modulus when verifying the result. 

Note that although the computation is modulo $p$, i.e. you compute $g^xh^r \bmod p$, the exponents $x,r$ are in $Z_q$. And so the operations among the exponents are modulo $q$. That means, after the homomorphic operation, you get a commitment of $x_1-x_2 \bmod q$, not $x_1-x_2 \bmod p$ .