Possible reasons: It could be harder to control a moving object then a stationary object. Yoda could have been tired from the fight or less focused. It could actually be harder to control larger objects (which makes sense as otherwise jedis could move mountains with the force), and Yoda actually meant that the size of the X-wing didn't matter as it was still small enough to be controlled by the force
Real reason: Dooku had to escape as it was in the script
