My opinion from the information you have given:
People are obsessed with drug interactions ( clash between medications) and realistically there are only a very few situations where these actually exist. it doesn't mean that a "new" adverse chemical reaction takes place which is detrimental to the patient, it just means that it affects the rate of absorption or action of a drug e.g anticoagulant.
In any case drug interaction doesn't apply to your case.
B12 deficiency:
I am going to assume that you are not anaemic.
I would stop taking the B12 tablets ( no harm will come to you) and see if your stomach pains and alteration of bowel movements disappear. if so, then do not take any more B12 until you see your doctor and then report your findings. If the symptoms persist, then it is not due to your B12 and I would venture a visit to your GP.