How does a CSU/UC transfer work when enrolled in two California community colleges?

I am enrolled in 2 community colleges in different college districts in San Diego. I am either planning to transfer to UCSD or SDSU. Both community colleges have different IGETC Matriculation, so I am confused on how it works for transfers and duplicate courses. Will they deny me because I took classes at different CC’s with different IGETC Matriculations? Has anyone ever done this before?