How can I fix my Honda SGX50 indicator/stop light problem?

I removed the wiring loom, having marked up what went where, replaced the indicators and plumbed it all back in again. The only problem is that when the indicators are on and the brake is squeezed the stop light flashes alternately with the indicators. There were no wiring instructions on the replacement indicators but I assume that it doesn't matter how you connect them up. What could I have done wrong?