SW4STM32 and SW4Linux fully supports the STM32MP1 asymmetric multicore Cortex/A7+M4 MPUs

   With System Workbench for Linux, Embedded Linux on the STM32MP1 family of MPUs from ST was never as simple to build and maintain, even for newcomers in the Linux world.
And, if you install System Workbench for Linux in System Workbench for STM32 you can seamlessly develop and debug asymmetric applications running partly on Linux, partly on the Cortex-M4.
You can get more information from the ac6-tools website and download two short videos (registration required) highlighting:

System Workbench for STM32

Breakpoint at the wrong line


Can you verify the project optimization and debugging settings ?

Go to the project properties > C/C++ Build > Settings > Tool Settings

In Optimization : set the optimization level to “None (-O0)”
In Debugging : set the debug level to “Maximum (-g3)”

Hope it is where the problem comes from.