I don't know if there's another thread describing this problem, but in past iOS's when I would reset the dictionary on my iPhone SE (i.e. Settings>General>Reset>Reset Keyboard Dictionary) my frequently used emojis would reset too. But, for some reason I've noticed ever since updating to iOS 10.3.1 when I reset my keyboard dictionary it doesn't clear my frequently used emojis now. If I reset my settings it will, but I don't want to go to all that trouble just to clear my emojis and return it to default settings since then I have to remember my settings for everything else (e.g. mail, safari, etc.). If this is a bug in the latest iOS hopefully it too (like all the other bugs) will be corrected in the next update