What version of Kibana and ES?
Does the total Count on the discover tab (top right corner) match the count you get when hitting Elasticsearch directly? If not, try opening developer tools in your browser and look at the requests Kibana is sending to elasticsearch. On the Discover tab you should see a couple of msearch requests. Are they querying the indexes you'd expect?
Also some info mentioned in this thread might be of use: Kibana not showing recent Elasticsearch data
Thanks
Rashmi