I've noticed it on two occasions so far, may update here if it keeps happening. Sometimes, when I open up green treasure boxes, the coins that pop out start despawning in seconds, right before my eyes. Both occasions coincidentally happened when I blasted them open with a bomb (Dark Briar Barrage), but that may or may not have anything to do with the problem. Most boxes I've opened, the coins seem to have the normal despawn time (I don't wait around, but they're there for the 5 seconds or so it takes to pick them up).

It's not a huge problem since usually you're right there when you open the boxes, but it's unexpected behavior and could have an impact if it is happening elsewhere.