Should be fixed by Loïc's recent change:

openssl (1.0.0e-2ubuntu2) oneiric; urgency=low

  * Unapply patch c_rehash-multi and comment it out in the series as it breaks
    parsing of certificates with CRLF line endings and other cases (see
    Debian #642314 for discussion), it also changes the semantics of c_rehash
    directories by requiring applications to parse hash link targets as files
    containing potentially *multiple* certificates rather than exactly one.
    LP: #855454.

 -- Loïc Minier <[email protected]>  Tue, 27 Sep 2011 18:13:07
+0200

** Changed in: openssl (Ubuntu Oneiric)
       Status: Triaged => Fix Released

** Changed in: openssl (Ubuntu Oneiric)
     Assignee: Colin Watson (cjwatson) => Loïc Minier (lool)

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https://bugs.launchpad.net/bugs/854927

Title:
  c_rehash creating bogus links to ca-certificates.crt

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