After relining complete denture for a patient, operator observes that patient has difficulty in biting with dentures. What could be the most possible reason?

During relining procedure, utmost care should be taken, so as not to alter centric occlusion. A  precaution for this would be, placement of both dentures while relining and working on one denture  at a time. Changed centric occlusion will result into faulty occlusion, which will then require either repeating procedure or by grinding of interfering contacts, if discrepancy is small.