You're being totally vague, so not sure what your problem is,
so I'll make a deduction:
You wanna use No$GBA saves on Pokegen or PKHeX, but not cannot be loaded.
If your save file size is too small(like 20-40KB range) for some ungodly reason,
edit your NO$GBA.INI file with notepad,
and change
SAV/SNA File Format == Compressed
to
SAV/SNA File Format == Raw