IF you have rather complex code modules THEN
IF your linker is set for default settings of "Remove Unused Sections" THEN
IF you debug your code THEN
the PSOC Creator debugger gets bad information and you are debugging in the wrong file.
endif
endif
endif
The FIX is to go into Menu Project -> Build Settings ... -> Dialog , goto Arm GCC 5.4 -> Linker -> Optimization and change "Remove Unused Sections" to False