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If Wireshark can successfully merge the files but mergecap can't, then there may be a bug in mergecap. I'd recommend filing a bug on the Wireshark Bug Tracker and attaching 2 sample capture files that can be successfully merged in Wireshark but that fail to be merged with mergecap.
Before filing a bug, you should make sure you're using the latest version of Wireshark, currently 3.2.5, in case this was a known bug that has already been fixed. You might want to include your Wireshark version information from Wireshark's Help -> About Wireshark -> Copy To Clipboard when you report problems here, but certainly do so if you open a bug for this.
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