How to prevent "Local transaction already has 1 non-XA Resource" exception?

Ok,

it's solved now. I'll share just in case somebody got tackled by similar thing. Whole problem was with netbeans deploying. They overwrite the settings in glassfish connection pool and when you set them proper at runtime, you got npe's or missing password silly stuff. The place to edit this is sun-resources.xml. XML element has attributes datasource-classname and rs-type. What needs to be done in case of Derby database is:

<jdbc-connection-pool ... 
        datasource-classname="org.apache.derby.jdbc.ClientXADataSource" 
        res-type="javax.sql.XADataSource">
   ...
</jdbc-connection-pool>

Works like a charm now.

I'm using 2 PU in stateless EJB and each of them is invoked on one method

Indeed. But you're calling the second method from the first one so you're doing a distributed transaction and you need to use XA for this (at least for one of the resource since GlassFish supports the last agent optimization allowing to involve one non-XA resource). In other words, setting one of your datasource as a XADataSource is the way to go.

If you get an error when doing this, please add details about what you did exactly and the stacktrace.