That is because the Y had to have come from the father.
This is how a maternal uncle and nephew might share some of their X chromosome.
Now let’s see what happens with a paternal uncle and nephew: Here we have the same sort of layout.
This normally wouldn’t happen with a nephew and uncle on the father’s side.
This is just one way that close relations might make it so the paternal uncle and nephew share DNA on their X chromosome.
This is because the X chromosome (or any other chromosome) from your common ancestor has probably been chopped and swapped along the jumps from one generation to the next.