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The second phase (the "Running" phase) consists of sorting out the cards that you collected from phase one and determining how far you progressed along your obstacle cards.
Maybe I do not remember the rules right, but I thought that the second phase consisted of just running the cards. You were not allowed to reorder your cards at all. You must have picked them up in order in phase one. On the first mistake you made, you stopped. Did I remember the rules wrong here?