What are these red boxed inside my JPA ER-diagram?

After adding persistence.xml :

<?xml version="1.0" encoding="UTF-8"?>
<persistence xmlns="http://java.sun.com/xml/ns/persistence" version="2.0">
    
    <persistence-unit name="NewPersistenceUnit"/>
</persistence>

Red boxed almost completely disappeared. But that should not be the case in the first place

Is it possible  to provide sample project example demonstrating the issue?

I can't provide the code, but I can tell what happened. The project has entities, that are managed with Spring Data and a lot of other stuff like LDAP, other services, and the whole front end. Then I did this: module > add framework support > JEE Persistence something (before that I've added hibernate but that option just does not see any entities, probably because we're using Spring Data and we don't have any configuration files concerning JPA, except the DB credentials in application.properties) > and it automatically created a folder META-INF and the persistence.xml (shown above) > I deleted the generated stuff > generated a ER diagram > saw the red boxes > posted here > undid the deletion and the boxes disappeared, but only for our entities, some Spring entities (2 entities) that the IDE recognized all point to red boxes.

I'm planning to actually delete the META-INF for production, because we don't need that.