We faced with such problem. When one of patch commands fails to execute properly(not first command), flyway does not throw any exceptions, and marks this patch as executed in schema_version table.
It can be reproduced in such way: just create patch with statements(should fail on ) to flyway-samle project and run it.
INSERT INTO test_user (name1) VALUES ('test');
INSERT INTO test_user (name1) VALUES ('test');
Patch should fail but it doesn't.
We investigated this problem and found reason of bug. On executing statement, JdbcTemplate uses execute method. But it would be better to use http://docs.oracle.com/javase/7/docs/api/java/sql/Statement.html#executeBatch%28%29