In one aspect, a method is performed by a computing system that is in communication with a content-presentation device, where the content-presentation device is scheduled to perform, at a modification start-time, a content-modification operation that comprises modifying a modifiable content-segment that the content-presentation device is scheduled to receive. The method includes determining that the content-presentation device has detected, within a predefined time period after the modification start-time and during performance of the content-modification operation, a mismatch between reference fingerprint data representing the modifiable content-segment and query fingerprint data representing content received by the content-presentation device from a tuner device connected to the content-presentation device. The method also includes determining that the mismatch is due to the tuner device having modified the modifiable content-segment before the modification start-time and, in response to determining that the mismatch is due to the tuner device having modified the modifiable content-segment before the modification start-time, performing an action.