For non-software examples look at the history of the laws of physics. Newtonian gravity worked great for many things, but at some point scientists noticed for example that the orbit of Mercury didn't drift as predicted. This was fixed with the theory of General Relativity, which could be said was "leaking through" with the orbit of Mercury.
However, this doesn't mean that the abstraction is useless. Newtonian gravity is much easier to work with and works just fine for many applications, which is why it's still widely taught and used. But at some point, you have to deal with the leaks, and for that you have to know relativity (or become a research physicist, since we now suspect relativity to have leaks of its own)