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Using Merge: Receiving Bad TCP Errors on Good Packets

After merging two pcapng files, from two different firewalls, I am receiving Bad TCP errors. These are retransmissions; spurious retransmissions; ACKed unseen segment; Previous segment not captured; Port numbers reused; etc. Is there any way to resolve this? Using WS v3.0.2/Win 8.1.

Thanks and God bless, Genesius