Crafting more than 1 honey block gives back only 4 bottles when shift left-click on the crafting output, but shift left-clicking on the crafting recipe does not do that.
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It also occurs in PS4 platform maybe it affects each bedrock version. Moreover, if you craft them one by one in PS4 you also lose some botles it only gives you 4.

Affects 1.14.1 Hotfix on iPadOS 13.3

This issue has been resolved in a Beta release. We will leave the ticket open for reference until the fix is migrated into the official release.

In the change log it says it is fixed. But in this Video a player crafts 64 honey bottles together and only gets 60 bottles back. https://youtu.be/sVmCnRQ2Tyw So it hasn't fully been fixed.

You can see it at 6:00

In Nintendo Switch version 1.14.20 it still happens, I crafted 4 honey blocks (16 Honey Bottle) and only got 4 back, I lost 12 bottles in the process

In the full release of 1.14.30 today this is still not fully fixed. It works as described by bugsbugsbugs above: crafting 16 honey with 64 honey bottles only returns 60 empty bottles to you.
More precisely, crafting honey blocks from the 2x2 grid only returns the bottles rather than consuming them if there is a non-full stack of honey blocks already in the inventory, or if there is a non-full stack of glass bottles in the inventory spot just before the next available one that the game would choose to put crafting products in. If there are no honey blocks or only full stacks of honey blocks in the player inventory, and no glass bottles or a full stack of glass bottles in the inventory spot before the next open one, then a honey block crafted from the 2x2 grid will consume its glass bottles. Actually, “overwrite” is probably more accurate than “consume,” because what appears to be happening is that the bottles are returned first, then the honey block is sent to the same inventory spot as the bottles because the inventory contents are not being updated in between the two crafting outputs.
Update: the same issue is also causing empty buckets to overwrite cake: MCPE-63228.

With further testing I've found that the bug is still more complicated.
The behavior described in the preceding comment , in which the first honey block crafted overwrites 4 bottles, only occurs in creative mode.
In survival mode the first bottles overwrite the honey block.
After testing these things for a few minutes, trying to craft stacks is now causing a single set of products to be thrown to the ground. In survival the honey block is overwritten and 4 bottles are thrown down, while in creative a honey block is thrown down with the 4 bottles. Also, when trying to put honey bottles in my inventory I have to shift-click twice each time. Videos of both behaviors attached.
Update: actually, I have to shift-click twice on the creative inventory to get any item into my inventory now, not just honey bottles. And I have to click twice on the creative inventory item to pick it up from the creative inventory.
Update 2: closing Minecraft and reloading resolved the inventory glitch. However it does seem to occur after trying to craft honey blocks from a crafting grid a few times in survival mode, as I experienced this on both Windows 10 and iOS.

Forgot to mention explicitly that the bug in 1.14.30 occurs from both the 3x3 and the 2x2 grids.
Also, it occurs to me that the behavior here of overwritten outputs that with successive iterations cause the entire player inventory to be glitchy, might be the result of a client/server disagreement, like what is happening with dispensed items in MCPE-60178.

Related to MCPE-63461?