You probably have too many shards per node. This is not a Kibana error, but rather an elasticsearch issue. You have failing or otherwise unavailable primary shards. May I suggest you look at the following resources about sizing:
You can set the time to 0 and get it to log every query. There are some config variables we can use to gain more control of log output. For posterity, here are some of the possible config values you could set, either in kibana.yml or via the command line when calling bin/kibana .
no output, don't even setup the logging output
Only log messages tagged with error or fatal tags, or errors caught by hapi
Log all the things, including information about system usage and every request
map of log types to the tags they should output. Supports * tag
provides access to every possible combination of logging output filtering. Also can add support for custom loggers setup by plugins, etc.