Natural products are very complicated mixtures. Occasionally you will find a single compound in high enough concentration to isolate, or that will have a very specific property that will allow a separation technique that will isolate it. More frequently, you will have the situation the Discodermolide reports - a method of isolation will give a complex mixture. In that case, any change in isolation conditions will result in changes in composition of the products, even if there are no chemical reactions. When you add the possibility of thermal reactions, the situation just gets more complicated.
Ideally, you adjust your separation technique to give you a suitable product, then try to make that technique as consistent as possible. Changes to the technique will change the product.