Two examples from my experience:
JSF is doing lots of "magic" trying to keep state. It isn't exactly quick to render a simple hello world page, but if you mess up the state on a somewhat complex page, JSF spends ages in it's six (yes, six!) lifecycle stages [0].
Hibernate is probably the worst offender. Well, the interface is somewhat nice: you don't have to care about loading objects from the database, Hibernate will load them for you. One object, one request at a time. Looking at the hundreds of generated SQL requests it's quite easy to figure out how you would write better SQL... but you don't write the SQL, Hibernate does :)
The lesson IMO is: If you're writing everything from scratch, language performance is important. If you're using frameworks, the performance of the whole stack is way more important and one should probably compare benchmarks - or even real-world applications that are similar to ones use case - of the whole stack.