Well I would be lead to speculate it is because you are using your anaerobic and aerobic systems together.
Stop training intervals with long distance. Two different energy systems within the body.
long distance one day and sprints or intervals another. The sprints or intervals will cause side stiches because it is anaerobic and burns the muscle out faster of glycogen and oxygen. The aerobic eventually will cause stitches as well but not nearly so quickly.
Are you training to be long distance or to lose and maintain fat percentage. If it is the later than stick to intervals, they work far better for fat loss and maintenance than long distance running.
join in guys if you have other oppinions or anything to add.