Are you using a monitor with an actual capnograph or just using a pulse oximeter that calculates respiratory rate based on fluctuations in hemoglobin saturation? The pulse ox-derived respiratory rate can be prone to errors, probably not in a small part due to the fact that pulse ox units themselves are prone to errors.
Honestly, I seldom rely on a monitor to determine respiratory rate... especially in an anesthetized animal (which I would assume it was if you're trying to use a monitor), they breathe slowly enough that I would probably just count respirations myself. When I do use a monitor to measure respiratory rate, a capnograph is my first choice.