Reproduction:
$JENKINS_HOME/plugins: subversion (directory), subversion.hpi
1) Open http://<root>/pluginManager. Update Subversion plugin from 1.34 -> 1.37 using download now and install after restart button.
$JENKINS_HOME/plugins: subversion (directory), subversion.bak (1.34), subversion.hpi.pinned, subversion.jpi (1.37)
2) Restart Tomcat/Jenkins
$JENKINS_HOME/plugins: subversion (directory), subversion.bak (1.34), subversion.hpi (1.34) subversion.hpi.pinned, subversion.jpi (1.37)
3) PluginManager still reports old version

Should note that the logs report:
INFO: Ignoring /ci/jenkins-home/plugins/subversion.jpi because /ci/jenkins-home/plugins/subversion.hpi is already loaded

Also the plugin is broken at this point with a NoClassDefFound on org/tmatesoft/svn/core/SVNException

Clean State:
1) /etc/init.d/tomcat7 stop
2) cd $JENKINS_HOME/plugins
3) rm subversion*
4) /etc/init.d/tomcat7 start

Workaround:
1) Restore clean state
2) Update plugin
3) Stop tomcat/jenkins
4) cd $JENKINS_HOME/plugins
5) mv subversion.jpi subversion.hpi
6) Start tomcat/jenkins