To re-produce you just need to use the https://wiki.jenkins-ci.org/display/JENKINS/GitHub+pull+request+builder+plugin and not use the "cron('H/5 * * * *')" as the documentation says.
Then, the following stacktrace is triggered:
Jun 23, 2016 10:35:00 AM hudson.triggers.Trigger$Cron doRun
WARNING: Cron thread throw an exception
java.lang.NullPointerException
at hudson.triggers.Trigger.checkTriggers(Trigger.java:267)
at hudson.triggers.Trigger$Cron.doRun(Trigger.java:221)
at hudson.triggers.SafeTimerTask.run(SafeTimerTask.java:50)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
at java.util.concurrent.FutureTask.runAndReset(FutureTask.java:308)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.access$301(ScheduledThreadPoolExecutor.java:180)
at java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask.run(ScheduledThreadPoolExecutor.java:294)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Any cron job on the instance will work because of this issue