I noticed a problem where Hibernate is returning stale date from the query cache if you add an element to a many-to-many relation and there are not other changes. In this case

Hibernate invalidates the query cache region for the many-to-many relation when the element is added
Checks the query cache regions for the two entity tables but completely ingores the cache region for the many-to-many table

2016-02-18 11:38:56 DEBUG UpdateTimestampsCache:87 - Pre-invalidating space [A_B], timestamp: 5962924018069504
2016-02-18 11:38:56 DEBUG UpdateTimestampsCache:123 - Invalidating space [A_B], timestamp: 5962923772317696

2016-02-18 11:39:12 DEBUG StandardQueryCache:155 - Checking cached query results in region: hibernate.test.org.hibernate.cache.internal.StandardQueryCache
2016-02-18 11:39:12 DEBUG StandardQueryCache:253 - Checking query spaces are up-to-date: [A, B]
2016-02-18 11:39:12 DEBUG UpdateTimestampsCache:171 - [A] last update timestamp: 5962923722252288, result set timestamp: 5962923722276865
2016-02-18 11:39:12 DEBUG UpdateTimestampsCache:171 - [B] last update timestamp: 5962923722252288, result set timestamp: 5962923722276865
2016-02-18 11:39:12 DEBUG StandardQueryCache:178 - Returning cached query results

I also noticed another similar problem: when I modify a many-to-many relation and run a query right after that Hibernate doesn't seem to autoflush this change and the query returns the old data. Once I modify another attribute of on of the entities or call flush() manually the query returns the correct data