There are many possible causes. The most common cause is an improperly degassed mobile phase with fluctuations in the flow rate as bubbles pass through the pump. You should be able to detect this by observing whether or not the pressure is stable or not. If it is not stable that I would focus on improving the degassing of your mobile phase or add some pressure to the source bottles. If the pressure is stable, another possible cause of the problem is thermal fluctuation. Is your column thermally isolated or in the open air? Good temperature control will eliminate this problem but if you don't have a column oven you can at least partially mitigate this problem by surrounding your column with readily available insulation.