Not a crime, but can be a pain in the arse, that is, if you seat the ball flush with the muzzle using a ball or short starter, before drawing the rod out.
If the rod is even with the muzzle when it is in the pipes and runs under the barrel to the front of the breech block, it will be sticking out the muzzle when the load is seated on the powder, by the length of the load (powder and patched ball) itself, thus is longer than needed to seat a ball and gives enough finger purchase to remove, etc.
With a rod of a length to not stick out past the muzzle when in the pipes is used for cleaning, by screwing a jag into a rod tip, the jag's length will make the rod that much longer than the bore needing cleaning, which also should give adequate finger purchase on the rod.
I've also seen pictures of rods sticking well out past the muzzle of the gun. They can be a pain when hunting, catching on branches, trees, underbrush, etc.
In the movie about hin, Alvin York's ram rod stuck well out past the muzzle of his rifle, while he was carrying it and when it was above the door (fireplace?) in the house. My memory's a bit foggy on that as It's been at least 45, maybe 55 years since I saw the movie - with Gary Cooper, I think, playing Alvin York.