Same problem here, using mapreduce in Matlab 2015b! The breakpoint is active when mapreduce is running, but Matlab doesn´t stop when running the codeline where the breakpoint is located in the mapper function.
Tried to reduce the parallel pool to just 1 worker but that didn´t help.
Any suggestions would be appreciated!
Found the answer myself: It seems that Matlab cannot consider breakpoints when using a parallel pool. So for me it helped to uncheck the option "Automatically create a parallel pool" in the preferences of the Parallel Computing Toolbox and shutting down all active parallel pools using