Can alveolar pCO2 exceed pulmonary end-capillary CO2? Yes.
In 1891 Christian Bohr observed that alveolar PCO2 could exceed arterial PCO2 when high levels of CO2 were present in the inspired air. He proposed that CO2 could be secreted by the lung. His hypothesis was dismissed as being due to experimental error; however, recently the same phenomenon was rediscovered using modern techniques. A possible explanation for the phenomenon may involve coupling between diffusion and chemical reaction of H+, HCO3-, and CO2 in the vicinity of a negatively charged capillary wall, causing the PCO2 to be higher near the wall that in the bulk phase of capillary blood.  Alveolar PCO2 is related to the PCO2 near the wall rather than the bulk phase PCO2. The Charged Membrane Hypotheses can explain the phenomenon of CO2 secretion not by a cellular mechanism, but a physical chemical disequilibrium within the capillary which is maintained by blood flow through the capillary.
D000818:Animals; D001639:Bicarbonates / Q000097:blood; D002196:Capillaries; D002199:Capillary Permeability; D002245:Carbon Dioxide / Q000097:blood / Q000378:metabolism*; D006801:Humans; D006863:Hydrogen-Ion Concentration; D010313:Partial Pressure; D005082:Physical Exertion; D011650:Pulmonary Alveoli / Q000098:blood supply / Q000502:physiology*; D011653:Pulmonary Diffusing Capacity; D012119:Respiration
D001639:Bicarbonates; D002245:Carbon Dioxide