1. A method, comprising: receiving, by a system including a processor, a first probe fingerprint associated with a probe media file from a client device; comparing, by the system, the first probe fingerprint to reference fingerprints associated with reference media files to identify matching reference fingerprints; in response to identifying the matching reference fingerprints, identifying, by the system, a set of discrepancy regions of the first probe fingerprint and the matching reference fingerprints comprising: comparing respective pairs of reference media files associated with the matching reference fingerprints, comprising comparing respective sequences of feature vectors associated with the reference media files using a distance measure, generating a similarity matrix by identifying an alignment between at least two reference media files of the pairs of reference media files, identifying time ranges at indices that do not match along a diagonal of the similarity matrix, and grouping the time ranges into a set of time ranges and determining a union of the time ranges in the set of time ranges to generate the set of discrepancy regions; communicating, by the system, to the client device a request for additional data regarding the probe media file associated with the set of discrepancy regions identified; receiving, by the system, the additional data regarding the probe media file in response to communicating the request.