Cross game transfer

Is there any way to transfer pokemon to yourself from
(Pokemon X) → (Pokemon omega ruby)
Through citra?

In order for us to provide better support, we need to see the log generated by Citra. This guide will walk you through how you can obtain the log file: How to Upload the Log File.

You don’t need to transfer, you can do a simple trade between Pokemon X/Y and Pokemon OR/AS.
This can be done through the multiplayer rooms. Either trade them to someone else first who trades them back to you, or open a second instance of Citra and trade with yourself.