If you encounter this situation in the real world, I suggest asking for clarification, such as, "Does that mean we can skip it, or that we'll fail?" Once you encounter the phrase many times, and always with the latter definition, updating would suggest that any future uses will have the same (not quite literal) meaning, allowing you to be more confident in your understanding. If there is still enough doubt remaining, then ask every time.

This method works even if you can't think of alternatives but realize that people don't always mean what they say. "Does that mean we can skip it?" is an adequate way to express, "This is my understanding of what action I am allowed to take without penalty; please check it and let me know if I am correct."

Encountering many situations where you require this question/answer method to determine what someone really means would show that it's a necessary component of understanding neurotypical communication. As someone who has problems with literal-mindedness, constantly asking questions and updating based on the responses changed my relationships significantly for the better.