Here's some elementary stuff (so that we don't get bogged down in unnecessary technicalities) to think about. Suppose we'd like to integrate something like $$\int_0^{\infty} {1 \over x^2} {\rm d}x.$$
This of course diverges but we can insert some regularizator $M$ that captures the divergence in the $M \to 0$ limit
$$I(M) := \int_0^{\infty} {1 \over (x + M)^2} {\rm d}x = \left[- {1 \over x + M} \right]_0^{\infty} = {1 \over M}.$$
We obviously can't change the value of $I(M)$ by using any (smooth) substitution. so, suppose we changed our original integral using $x = y^2$. Then we need to evaluate
(Edit: there was a mistake in this calculation that changes the result of the discussion).
$$\int_0^{\infty} {2 \over y^3} {\rm d}y$$
and using the same regularization procedure $x \to x + M$ or $y \to \sqrt{y^2 + M}$ we get
$$I(M) = \int_0^{\infty} {2 \over (y^2 + M)^{3/2}} {\rm d}y = \int_M^{\infty} {1 \over z^2} {\rm d}y = {1 \over M} .$$
On the other hand if we naively performed the regularization $y \to y + M$ we would obtain a different result
$$I(M) = \int_0^{\infty} {2 \over (y + M)^3} {\rm d}y = {1 \over M^2} .$$
So I guess the point is that one needs to make a regularization that respects the substitution to obtain consistent results.