Don't forget that you also charge the runner with a "caught stealing" in that situation.
As a matter of practice, though, you normally credit a stolen base unless he was really out "dead to rights" and the infielder really just muffed it. You wouldn't give an E on a bang-bang play nor if the runner kicked the ball out of the glove. But if the throw is there well ahead of the runner, hits the infielder's glove on the fly and is just plain dropped, then you can charge the E.