Mkvmerge has 2 different --append-mode settings. It's common for the default setting to create audio or video gaps. You can read in the docs about them:
https://mkvtoolnix.download/doc/mkvmerge.html
Quote:
Originally Posted by Perenista
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It says video is 48m39s, audio is 48m38s. If you use the default append mode a 1 second audio gap is expected. (Feature, not bug.)