How I Met Everyone Else - S3-E5
Continuity mistake: During the flashback in which Barney recounts the story of how he and Ted met (which was previously shown in the pilot episode of the series), there is a green circular plaque (that reads "Winner of the Queen Cup") on the wall in the background which wasn't present in the pilot episode. Also, Barney's left arm is in different positions than it was in the pilot.
Answer: After running the marathon for Marshall with no training, he's allowed to ride the subway for free. While sat on the train, the muscles in his legs start to seize up after the marathon to the point it is painful to move his legs. This is why he can't move them. It's the same reason your body aches after a good session at the gym the day before.
Ssiscool ★