No. Pradaxa is a relatively new anticoagulant. At this time it does not appear to have any less effect when combined with pantoprazole. We know that some people who take plavix (clopidogrel) (anti platelet)have less effect of the plavix (clopidogrel) when they are taking the panyoprazol but this was determined years after the drug was being used.
There are issues. That can arise as Protonix (pantoprazole) can lead to decreased metabolites of Pradaxa and decreased anticoagulation affect. You may want to review this with your cardiologist or whoever is prescribing your anticoagulation to make sure he/she is aware of all the medications that you are taking.