I confirm this bug (too many files opened error message) on Ubuntu
6.06/Evolution 2.6.1 when training bogofilter with CTRL-Y on junk
folder's mails.

The filter rule used is :
    <rule grouping="all" source="incoming">
      <title>TeachBogofilterSpam</title>
      <partset>
        <part name="status">
          <value name="match-type" type="option" value="is"/>
          <value name="flag" type="option" value="Junk"/>
        </part>
      </partset>
      <actionset>
        <part name="pipe">
          <value name="command" type="command">
            <command>/usr/bin/bogofilter -s</command>
          </value>
        </part>
      </actionset>
    </rule>

-- 
too many files/pipes open
https://bugs.launchpad.net/bugs/60577
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