A: Magnesium citrate may cause some people to wake up in the middle of the night between 2:00 and 3:00. While for other people that may happen with Magnesium glycinate. Not eating enough carbohydrates throughout the day may also cause that. So, if you've changed your diet, this might be something to look into as well. Another reason for waking up between 2:00 and 3:00 could be due to blood sugar imbalance.
During the program you might have lowered your carbs a little too much. We do need carbs to help us produce our beneficial neurotransmitters and l-tryptophan. So, consider having some more carbs at bedtime, and see how you feel with that.