It manifests itself by the following messages that might linger in the log files for a while after upgrade if x-pack is installed.
[2017-09-13T13:24:57,961][INFO ][o.e.c.m.TemplateUpgradeService] [node1] Starting template upgrade to version 5.6.0, 2 templates will be updated and 0 will be removed
[2017-09-13T13:24:57,985][INFO ][o.e.c.m.TemplateUpgradeService] [node1] Finished upgrading templates to version 5.6.0
The problem is occurring because during application of templates the order of elements in the template mapping can get shuffled causing the follow-up check if update is need to fail. I am working on the fix.