I'm marking this as a dupe of bug 1422891. While this bug is around webm, I believe the crux of this issue if we choose to support .mkv. Webm is largely a constrained form of Matroska, but Chrome have been choosing to relax their constraints on handling Webms such that they're now handling what is (IMO) essentially mkv files.
Bug 1551765 Comment 12 Edit History
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I'm marking this as a dupe of bug 1422891. While this bug is around webm, I believe the crux of this issue if we choose to support .mkv. Webm is largely a constrained form of Matroska, but Chrome have been choosing to relax their constraints on handling Webms such that they're now handling what is (IMO) essentially mkv files. So in order to support these kinds of files we're going to need to at least in part support mkv.