Travelling by TARDIS isn’t always completely safe. Safer than most forms of travel, true, but even a living spaceship can’t predict every eventuality. Nor can an over nine hundred-year-old Time Lord. Besides, some incidents are just so unbelievable that it wouldn’t cross the mind of even the smartest person in the universe to consider them.
When you’re way out in the depths of space, getting hit by a boat definitely falls into that category. But there it is, the bow of a ship sticking right through the wall of the TARDIS. Complete with a lifebelt.
The Doctor’s understandably confused.