///////////////////////////////// test.d ////////////////////////////////
struct A
{
    int i;
    ref inout(int) opIndex(size_t idx) inout return { return i; }
}

struct B
{
    A[1] a;
    ref inout(int) opIndex(size_t idx) inout return { return a[0][idx]; }
}

bool ctfeFunc()
{
    A a;
    a[0] = 42;
    assert(a[0] == 42); // OK

    B b;
    b[0] = 42;
    assert(b[0] == 42); // fails

    return true;
}
enum eval = ctfeFunc();

unittest
{
    ctfeFunc(); // succeeds at runtime
}
/////////////////////////////////////////////////////////////////////////

It looks like the assignment is going into some rvalue which is then lost.