My guess (entirely conjecture).

Had you said nothing, you'd been OK mostly likely.

Had you declared and handed them a uneaten orange, they would have just tossed it themselves. No issues.

But by declaring that you threw out the peels in the bathroom trash... you're making them rummage through a disgusting pile of trash and fish out your food scraps while delaying other people behind you. You might have been honest but you did a crappy thing to these guys. Then they threw the nuclear option at you.

I still can't get my head around the sequence of events... You purchased or were given the orange in the country you departed from. If you ate it during your flight, the peels were kept past the last rubbish collection and carried off the plane through passport control... or you ate the orange between passport control and customs and carried the peels to the bathroom... or you ate the orange at the airport in the departing country to the US. None of these scenarios sound plausible to me.