Why can't we use one counterexample as the contradiction to the contradicting statement?
Example: Let a statement be A where a-->b. We can prove A is not true by finding a counter example.
Now, in another space and time, Let a new statement be B where it is the same as a-->not b.
Why can't we prove B is not true by finding a counter example? Thus, a contradiction and A is true?
Instead of having both $A$, $B$, $a$ and $b$, let's make some of them $p$ and $q$.
Also, since you're talking about counterexamples, there must be a quantifier somewhere, so I guess you actually mean something like
$$ A \equiv \forall x\,(p(x)\to q(x)) $$ $$ B \equiv \forall x\,(p(x)\to \neg q(x)) $$
Having a counterexample to $A$ means that we have a particular $x_0$ such that $p(x_0)$ is true but $q(x_0)$ is false.
Similarly, having a counterexample to $B$ means that we have an $x_1$ such that $p(x_1)$ is true and $q(x_1)$ is also true.
There's no contradiction in having both counterexamples at the same time, because $x_0$ and $x_1$ will in general be different things -- as evidenced by the fact that $q$ is false for one of them and true for the other.
And also,just knowing these two counterexamples doesn't tell us anything about whether $p(x)$ is true for any other $x$, different from $x_0$ and $x_1$. There may be lots of other $x$s that $p$ is false for. Or there might not -- the example doesn't tell us anything either way.