Hi Sumesh,
did you already have an Elasticsearch installation with Wazuh data? it's not as simple to transition because in version 3.0 our alerts mapping has changed (now user defined fields, along with some others, go into a structure called data) and you will probably have to reindex your data.
Also the whole configuration for the Elastic Stack has changed to reflect that so you are probably including something wrong at some point in the data flow, for example, Logstash no longer uses a template in its configuration.
Regards.