We are using NetBeans 8.1 (in Netbeans 8.0.2 we suffer the same bug) for a project with multiple JSP and, after setting breakpoints at some parts of the code, it decided not to stop at them while debugging. The most interesting part is that it worked last week normally, so I can't find any sense in this sudden failure. Example: we added an alert to check its functioning and put a breakpoint on it. When debugging this alert appears, but in NetBeans debug has done nothing (totally ignored breakpoints and can't use any button like "step over" or "continue", only "pause" and "stop" can be pressed).
If someone knows how to deal with this problem, please help us, we are in a hurry to continue the project and we haven't find any post with a similar bug.