Hi meg2009Arm,
Don't know about sitagliptin, but metformin is known to cause trouble with digestion and intestinal function. Many people find that the slow release version (sometimes called SR, extended release ER, or modified release MR) is easier on the stomach. Also do you take your metformin with food? Some people have said that this helps.
I would ask your foctor for the slow release version and see if that helps. Of course it could also be due to other problems, such as IBS, IBD etc. so I would go back to your GP and make it clear that this is causing a real issue for you and you need to do something about it.