I agree a debugger can help you figure out mysteries. But when I find myself using one, I try to ask: how could I have avoided having a mystery in the first place. Common answers: better tests, cleaner code, better design.
I wouldn't be so keen to say that these help "avoid mysteries" in the first place. Many algorithms that have better time complexity and space complexity are often much harder to understand than writing algorithms that sacrifice those qualities, but can be understood at first glance. For example, is it easier to understand code that performs a lot of bit wise operations, which is probably better designed and more cleaner than a piece of code that performs operations with strings and object?