Can Berberine cause upset stomach?

Berberine in particular is known to cause some digestive upset for some people, so I would suggest the following: 

To do some detective work to find out if it is Berberine or perhaps another particular supplement that is bothering you, stop all supplements for a few days, and then add one back in at a time. Start with berberine, take only Berberine for 3 days, and see how you do. If there are no problems, continue taking it and add in one of the others for 3 days, etc. If you do experience upset, stop taking the berberine, give your body another break for 2-3 days, then introduce another one of the supplements to see how your body does.

If you do pinpoint one supplement that seems to be problematic, you can try cutting the dose in half and/or taking it every other day.