Missy, the book explains what happens when you eat things with a high glycemic index. Your body responds in a rapid (and crazy) way and stores the extra sugar as fat. In addition, you often end up with some water gain. Your fat cells never go away, they just shrink down. They love to fill up with water at any given chance. On SBD, you can gain rapidly during a planned treat, but you lose it just as quickly once you detox again. Drinking lots of water will help mitigate this effect.
I wouldn't let this deter you from the plan. I haven't heard of anyone having trouble with weight gain in Phase 3 unless they overate or went off plan for a long time.