Some are simply due to the conditions we paddle in being the effect of wind and waves. But unfortunately by far the most common is to do with paddling technique. This article deals more to do with that aspect . More about wind and waves in another article.
Before going into a lot of detailed paddling technique a bit of hydo mechanics may explain why it wonders over the waters as such.
As a vessel travels through the water there are two forces acting on the hull. At the front (bow) there is pressure on the hull as it pushes water out of the way. This is evident from the bow wave or wake forming. Also at the same time at the back (stern) of the boat the water is rushing in filling in the void. With equal positive pressure on both sides of the bow balanced by an equal negative pressure (suction) on both sides of the stern the kayak ought to track nicely. When that pressure balance on the stern of the kayak is upset the stern will move sideways towards the side of less pressure. Stern goes one direction, the bow goes in the opposite direction.
This nice balance is generally upset by pushing more water (with the paddle blade) to one side of the stern of the kayak than the other. Given that almost none of us paddle perfectly evenly on both sides it stands to reason that we will cause a bias on one side and so cause a difference in pressure, thereby causing the kayak to veer off course.
In the article on forward power paddling strokes, it cannot be over emphasised the importance of keeping the stroke short. That is, the paddle blade ought not to travel past the thigh. If it does then water is pushed back and towards the stern of the hull causing the nice balance in lower pressure (suction) to be disturbed. Hence making the kayak turn by the stern.
Once that pressure balance is upset the kayak will create its own momentum and turn even faster, making it even more difficult to correct course. Many paddlers attempt to correct this using a not so well performed sweep stroke which only adds to the problem. That is driving more forward motion causing more suction and then disturbing the balance of pressure causing more turning. So the answer is simple. Keep the paddle blade in front of the thighs. Catch ought to be as far forward as possible and exit at the thigh.
This principle of equal pressures and suction explains a number of issues when paddling a kayak. Such as why it is possible to change direction with a “J” lean simply by leaning, or edging the kayak to one side while paddling evenly forward. Or how to overcome weather cocking in windy and or choppy conditions. Remember, resistance to forward motion is not just about the pressure of moving water out of the way and the front.
It is also about the suction forces acting on the stern of the kayak. More about this in articles on kayak design.