I had the same problem with the 2 EJBs too. The fact is that the WAR has a reference on the EJB-jar and copies the JAR into the /lib of the WAR-file. Since GFv3 scans the /lib of the WAR, it deploys also the EJB in the WAR file.
You must make sure that the EJB is not copied into the /lib directory of the WAR. Netbeans already takes care of this (with ANT). Only Maven is not that smart and copies the EJB into the WAR. I hope they will fix this soon. The same goes for the Webservices. It works with ANT, but not with Maven. But there I have other problems.
Greetings
Jan
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