When connection.stop() is called, the JMS client should release all it's messages in the prefetch buffer.
For all we know, the connection may never be started (depending on application logic) and those messages will be stuck on the prefetch buffer. Releasing it will allow another consumer to get them (in the case of a shared queue case).
Another less severe but nevertheless an undesirable side affect of this is the client getting more messages than required by the capacity or prefetch arguments. See QPID-3602
This may not be a big issue if the client is prefetching a few messages, but if prefetching something like 5000 messages, this could potentially cause a lethal spike in the clients memory usage.
Even in low capacity/prefetch values, if the messages are large (say in the mega byte range) this could potentially put the client under memory pressure.