I'm also seeing this bug.

Since /usr/bin/epubcheck is a symlink to /usr/share/java/epubcheck.jar and running

   java -jar /usr/share/java/epubcheck.jar

runs epubcheck fine, I think the obvious solution is to replace the symlink with a small shell script.
Here's a suggestion:

   #!/bin/sh

   exec java -jar /usr/share/java/epubcheck.jar "$@"

The executable permissions should also be removed from the jar-file. Having jar as an executable format may have worked at some point, but not any more.

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