We currently have a limit of 30 Cloud SQL connections per App Engine app instance (see the Warning from [1]) but that restriction can sometimes be applied to a total number of connections from a subset of those. This will be fixed in the App Engine 1.9.5 release when a strict per App Engine instance limiting will be rolled out. Sorry for the pain. :-(
[1] https://developers.google.com/appengine/docs/java/cloud-sql/#Java_Connect_to_your_database