Have experienced it twice- once in NDLS bound Shramjeevi Express and another time in Bareilly Bound Ala Hazrat Express.
In first case, AC-1 CNF berth was booked but on charting berth was allotted in AC_2 as HA coach did not arrive at LKO from originating station. In second case, had CNF AC-2 berth. However on charting it was berthed in AB (composite coach) and berth was allotted in AC-3 part. When questioned, the authorities replied that the particular coach did not arrive from Zone originating the train - ECR and NR respectively. However, in both cases, managed to get refund of excess fare.