After update hibernate from 4.1.8.Final to 4.3.0.Final tomcat jdbc-pool start throwing this exceptions.
Next block contains AbstractQueryReport code, lines between 215 and 226
So looks like the code at 9ce5c32dd7d11bc13c659f98ee4cc29b26c2e70e it's not jdbc-pool friendly. Specifically the line JdbcCoordinatorImpl.java:399
To reproduce the exceptions just add some interceptor. For example add the next line to your server.xml resource configuration.
The exception in this description was thrown by the ResetAbandonedTimer interceptor.