It's not a common side effect but diarrhea has been mentioned as a reason for people failing to complete Green Tea research trials.
However it is worth persisting with.
Green tea is anti inflammatory , anti microbial and anti fungal, if as part of your induction you have also changed to Coconut oil (with similar properties) you will inevitably be getting some die off of pathogenic gut flora or candida, it takes a while to introduce and establish new gut flora so perhaps go easy on the green tea but persist. It may be worth taking a probiotic for 3~4 weeks.

Nephropal has a post today that shows one of the ways Green Tea influences metabolism. There is plenty of other research showing it's beneficial effects.