result.ptr[dim - 1] &= ~(~0 << (len & (bitsPerSizeT-1)));
On 64 bit machine 0 - is 32 bit value, but bitsPerSizeT == 64.

Need add cast 0 to size_t:
result.ptr[dim - 1] &= ~(~cast(size_t)0 << (len & (bitsPerSizeT-1)));


Test:
       foreach (len; 1 .. 256)
        {
            foreach (i; 0 .. len)
            {
                BitArray a1; a1.length = len;
                foreach (j; 0 .. len)
                {
                    a1[j] = true;
                }

                a1[i] = false;

                BitArray a2; a2.length = len;
                a2[i] = true;
                BitArray a3 = ~a2;

                assert(a3 == a1);
            }
        }

For reproduce you need fix opEquals (see bug #10948: http://d.puremagic.com/issues/show_bug.cgi?id=10948)