Are you using PSoC Creator to download the code?
In PSoC Creator, it would always program both cm0+ and cm4 no matter which you click, cm0+ or cm4.
Yes, we are using PSoC creator.
And for PSoC programmer, there is no option to program separate core in that what can be behavior ?
Both cores access the same memory (Flash and RAM) If you program the Flash you will always program for both cores, regardless if there is a selection or not.
That said, there are ways to do only partial memory updates that could only affect a single core, but this is not the standard approach done by Cypress tools.