When i cut down trees and bushes with a full inventory (stacks not full!), nothing drops but the tree disapears anyway and nothing drops to collect either.
I noticed this happens when the amount of one item collected from a plant surpasses the available invetory space, nothing from that plant will be collected and the plant just disappears.
As i got close to full inventory with leaves and tried to collect more from bushes it also became more difficult to even make a bush "disappear" but was still able to, when i spammed the collect-key a bit. Also the the framerate stuttered mildly when i ran around and tried to collect bushes under these conditions.
I also once dropped a stack of 498 leaves( wasnt able to max it out), then collected some more and when i picked up the stack again, the number was still 498, so the game deleted the previous amount (~20) and ignored the space for two more leaves also.
Dont know if that happens with limestone too, which drops sometimes from trees (im still not shure if it should)