It's happened to me twice. One the convenience store shop/small purchase. I went for a fountain drink for 99 cents. Got up to the counter and the cashier asks if that's all I'm buying, I say yes he says "Well today is your lucky day, it's on us."
They said they get to the point where the take a penny/leave a penny tub gets full of change, thy have to empty it and don't want to be over on the cash register, so they just give away an item. Good for them, but it made my work longer. I explained, no issues on the report.
Second was a 5Guys with required milkshake, first one I did. Shakes were new to this store and they gave away a few. FORTUNATELY in this case, he rang it up on the receipt but marked it as a manager's special discount. I'm not sure how that MSC would have responded otherwise.
But in most cases, if and items not rung up, I just note it in the report if possible.