In more realistic terms, I think what happens is that at the time when the mushroom/collectible would have disappeared off the ground, or shortly thereafter, it also disappears when the child is carrying it. Ordinarily, they can get it where it's going with plenty of time to spare, but if they get "stuck" someplace, it's more likely.

I've had it happen even without them being stuck, though, most often when a child is trying to get a collectible from the very bottom of the screen all the way to the research hut. Very frustrating.
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My setup: WinXP/Athlon 64 3500+/1gb RAM/DirectX 9.0c/128mb VRAM