The response (from Duhem, Quine and others) is this: Suppose you think A contradicts B. You would surely admit that, there is likely some other C that, if C were true, A wouldn't contradict B. But if that's the "logic" of science then it isn't straightforward deduction.

If you want an example, consider an ordinary empirical observation. Someone claims the ball is red; you look and you see green. Classic contradiction, right? Except if lighting conditions are wrong, or there is a pane of colored glass between you, or.. The point is that there are additional claims that, if they were true, would remove the "contradicts" relation between the two original claims. But ordinary logical relationships shouldn't work like that.