I had opened this issue in Wildfly's site:
https://issues.jboss.org/browse/WFLY-9739

I'm getting an Exception as a warning in the server.log when a database object already exists an my persistence.xml has the property "hibernate.hbm2ddl.auto" set to "update".

This happen when deployed in Wildfly 11.0.0.Final (hibernate-entitymanager-5.1.10.Final).
This doesn't happen in my tests with Wildfly 10.1.0.Final (hibernate-entitymanager-5.0.10.Final).

Appearently, despite these Exceptions, all my applications are running ok.

This behaviour isn't good cause, I'm flooding the logs and it doesn't seem reliable for my manager.

Sorry for the copy/paste from my Wildfly's issue.

Steps to reproduce:

• Create a database [wildfly11-migration] in SQL Server 2014
• Create a datasource in standalone-full.xml (jndi: java:/datasources/Wildfly11MigrationDS) using a sqljdbc4.jar driver
• Deploy the driver "sqljdbc4.jar" in Wildfly 10.1.0.Final (Hibernate 5.0.10.Final)
• Deploy the attached wildfly11-migration.war in the Wildfly 10.1.0.Final (Hibernate 5.0.10.Final)
• See that there is a table "Animal" in the database
• Deploy again and see that nothing special happens

• Repeat all the steps above but in a Wildfly 11.0.0.Final (Hibernate 5.1.10.Final)
• In the last step, redeploying, see a warning:
  2018-01-26 18:48:55,198 WARN [org.hibernate.tool.schema.internal.ExceptionHandlerLoggedImpl] (ServerService Thread Pool – 162) GenerationTarget encountered exception accepting command : Error executing DDL via JDBC Statement: org.hibernate.tool.schema.spi.CommandAcceptanceException: Error executing DDL via JDBC Statement
  at org.hibernate.tool.schema.internal.exec.GenerationTargetToDatabase.accept(GenerationTargetToDatabase.java:67)
  at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.applySqlString(AbstractSchemaMigrator.java:524)
  at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.applySqlStrings(AbstractSchemaMigrator.java:470)
  at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.createTable(AbstractSchemaMigrator.java:273)
  at org.hibernate.tool.schema.internal.GroupedSchemaMigratorImpl.performTablesMigration(GroupedSchemaMigratorImpl.java:71)
  at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.performMigration(AbstractSchemaMigrator.java:203)
  at org.hibernate.tool.schema.internal.AbstractSchemaMigrator.doMigration(AbstractSchemaMigrator.java:110)
  at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.performDatabaseAction(SchemaManagementToolCoordinator.java:176)
  at org.hibernate.tool.schema.spi.SchemaManagementToolCoordinator.process(SchemaManagementToolCoordinator.java:65)
  at org.hibernate.internal.SessionFactoryImpl.<init>(SessionFactoryImpl.java:476)
  at org.hibernate.boot.internal.SessionFactoryBuilderImpl.build(SessionFactoryBuilderImpl.java:422)
  at org.hibernate.jpa.boot.internal.EntityManagerFactoryBuilderImpl.build(EntityManagerFactoryBuilderImpl.java:880)
  at org.jboss.as.jpa.hibernate5.TwoPhaseBootstrapImpl.build(TwoPhaseBootstrapImpl.java:44)
  at org.jboss.as.jpa.service.PersistenceUnitServiceImpl$1$1.run(PersistenceUnitServiceImpl.java:167)
  at org.jboss.as.jpa.service.PersistenceUnitServiceImpl$1$1.run(PersistenceUnitServiceImpl.java:125)
  at org.wildfly.security.manager.WildFlySecurityManager.doChecked(WildFlySecurityManager.java:640)
  at org.jboss.as.jpa.service.PersistenceUnitServiceImpl$1.run(PersistenceUnitServiceImpl.java:209)
  at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
  at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
  at java.lang.Thread.run(Thread.java:745)
  at org.jboss.threads.JBossThread.run(JBossThread.java:320)
  Caused by: com.microsoft.sqlserver.jdbc.SQLServerException: There is already an object named 'Animal' in the database.
  at com.microsoft.sqlserver.jdbc.SQLServerException.makeFromDatabaseError(SQLServerException.java:216)
  at com.microsoft.sqlserver.jdbc.SQLServerStatement.getNextResult(SQLServerStatement.java:1515)
  at com.microsoft.sqlserver.jdbc.SQLServerStatement.doExecuteStatement(SQLServerStatement.java:792)
  at com.microsoft.sqlserver.jdbc.SQLServerStatement$StmtExecCmd.doExecute(SQLServerStatement.java:689)
  at com.microsoft.sqlserver.jdbc.TDSCommand.execute(IOBuffer.java:5696)
  at com.microsoft.sqlserver.jdbc.SQLServerConnection.executeCommand(SQLServerConnection.java:1715)
  at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeCommand(SQLServerStatement.java:180)
  at com.microsoft.sqlserver.jdbc.SQLServerStatement.executeStatement(SQLServerStatement.java:155)
  at com.microsoft.sqlserver.jdbc.SQLServerStatement.execute(SQLServerStatement.java:662)
  at org.jboss.jca.adapters.jdbc.WrappedStatement.execute(WrappedStatement.java:198)
  at org.hibernate.tool.schema.internal.exec.GenerationTargetToDatabase.accept(GenerationTargetToDatabase.java:54)
  ... 20 more