Rip subroutines out of the XS and replace them with Perl dummies. You can even do that without changing your Perl code:

use My::XS::Module;

*My::XS::Module::xs_subroutine_1 = sub {
    # a dummy
};

*My::XS::Module::xs_subroutine_2 = sub {
    return 0; # always OK
};
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That way, you can reduce the complexity as long as you have a test case that reproduces the error.

My personal guess, without seeing code, is that somewhere you don't POP enough elements of the argument stack, or have a mismatched ENTER / LEAVE pair.