What you were expecting to happen, and what actually happened:
Played the first Guild Wars battle today with my pure red team, winning easily. The victory screen then changed the team to the Explore team I had been playing previously, granting much less points due to mismatched colors.
Steps to make it happen again
Not sure, the only uncommon thing I did between Explore and Guild Wars was reconnecting to the chat. Whatever is causing it, it can likely be exploited in an inverse way, playing Guild Wars with an easy mixed color team, then getting credit for a matched color team to significantly improve scores.