When utilizing Redstone circuit to collect honey, bottle dispense to ground and can not be picked up.
Beehive with Redstone comparator on the back, leads to 6 redstone dust up to a stick piston above. Once activated, the Stick piston pushes a Redstone block above a dispenser that is above the beehive (redstone repeater right before the sticky piston, set to 2 ticks). Hopper in front of Dispenser to fill dispenser with bottles from shulker box.
Hoppers below beehive (right below or 1 block down, didn't make a difference) to collect bottles.
Had issue with bottles popping out the back of the dispenser, so i put upside-down stairs on the back of the dispensers to push the bottle out the front or bottom of the beehive.
Also tried placing trap doors i block in front of the beehive to try and guide the bottles down into the hoppers.
Bottles will pop out filled with honey, but can not be picked up by hand or by the hoppers. Bottles will naturally de-spawn after set amount of time.
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GoldenHelmet
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I think your setup and experience duplicates MCPE-58866. When testing that one I found that a dispenser facing downwards into a solid block (such as a beehive) will glitch items out the side of the block, not through the block into a hopper. I suggest you try a different design.
Also take a look at the comment on MCPE-60178. Items that glitch through blocks appear to be located in different positions than where they actually are. That is why you can't pick up those honey bottles by hand.