We know from Hatcher that ${H}_0(X,A) = 0$ iff $A$ meets every path component of $X$. A simpler case is that if $X$ is path-connected and $A$ is non-empty, then the first homology of the pair is zero.
I am not understanding where the following argument is wrong: $X=D^2$ is path-connected as contractible, $A=S^{1}$ is path-connected and meets the only path-component of $D^2$. Thus we should have $H_0(D^2, S^1)=0$ but we know that $D^2/S^1$ is homeomorphic to $S^2$, which has non-trivial $0-$th homology. Where do I go wrong?
EDIT: is it because the relative homology of a pair $(X,A)$ is not the homology of the quotient $X/A$?