I logged into the game and had full raid flags. I used all six, winning most. As soon as I went back to my stronghold I was alerted about an enemy revenge where I lost. The watchtower said it had happened 12 minutes ago, which is approximately when I started raiding.
I then noticed my trophy count had fallen significantly more than what I lost in the revenge. However, my alliance lists me as having many more trophies (over 100 difference). Even after reloading the game my watch tower count is lower than alliance list.
Based on offered trophies for a win/loss, I am guessing this is only a cosmetic issue which will resolve after my next raid, but wanted to report it.
Edit: I did a raid just to see if it would correct the mismatch… And it did.