I haven't verified in the latest version, but at least as of a few versions ago, using multiple Loyalty-gaining abilities on a character in one day could cause the "already gained loyalty today" flag to be set multiple times. Then when the day ticked over, one of those flags would be cleared, but not all of them, so the game would still think that they had gained loyalty the current day (and if you tried again on the new day, you'd end up adding *another* flag).
You can potentially clear the flags by waiting multiple days without attempting to use any Loyalty-gaining abilities on that character (I believe abilities that change their loyalty gain rather than giving a lump sum of loyalty are exempt, so you can potentially use abilities like Serve/Allure to keep their obedience up). Or you can clear the flags by mucking around with the save file, which is how I discovered that this was happening... <.< >.>
@Strive4Power suggestion: maybe have some UI indication of whether or not a character has gained Loyalty today? Nice game, btw.