It seems some (all?) wfShellExec errors end up in the HHVM fatal log, which is quite useless as it contains neither a stack trace nor wiki/URL information. These errors should be reported by wfShellExec via Monolog.
One example is T157644: Shell error from "pdftotext" and "pdfinfo" commands (e.g. "Syntax Error: Invalid XRef entry"); IIRC this was discussed in the past in the context of T111441: SiteConfiguration::getConfig() does not work in Wikimedia production but I can't remember the details.