Breakpoints in Eclipse

I built ES from its sources and ran it in debug mode from Eclipse.
I now want to add some breakpoints in order to understand how does ES work under the hood but some of them work and some others don't.
For example, I can set a breakpoint in method handleRequest of org.elasticsearch.rest.action.search.RestSearchAction and I see that it stops when I run a query.
But when I add some breakpoints in method hitExecute of org.elasticsearch.search.highlight.HighlightPhase, Eclipse does not stop if I run an highlighted query. I am pretty that this method is called because it throws an Exception that I can see in logs if I run an incorrect query.
Has anybody ever encountered this problem?

Thanks