In #1, we don't have enough information to decide if he's done exercising or not. People often continue exercising even when they're tired, so we don't really have anything to eliminate the possibility that he's still continuing to exercise. We get the phrase 'feel the burn' from this concept of continuing to exercise while we feel its effects. Ergo, there's just as good a possibility that he's still running as that he has stopped.
In #2, as Piscean and GoesStation mentioned, she's no longer running because she has reached her destination. It's highly unlikely that she's continuing to run in circles inside the church.
So you can see it's contextual clues that help determine whether or not the action is ongoing.
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