Steps to reproduce:
Start a single-player creative world.
Place a cobweb above a funnel with 1 block gap.
Drop an item into the cobweb.
The item will vanish into the funnel's inventory without ever falling out of the cobweb.
This appears to be a case of the hopper claiming any item in the space 1 block above itself, rather than waiting for the item to actually touch the hopper.
Items dropping in at normal falling rates seem to drop in reasonably — I suspect that in that case, the problem is masked either by a time delay or by server/client desync (which seems to be a problem for items lately; I keep seeing them jumping around, ever since the update which changed items-popping-out-of-blocks behavior).
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That is quite plausible, but the range doesn't need to be this big. Here's a couple other rules which could get the desired results without this quirk, and I am guessing would not be especially difficult to implement:
Items check if they are resting on top of a hopper block, and go into it if so.
The hopper's rim is zero-width, for item entities only, so items fall right in.
Confirmed in 13w02b.
Also confirmed. They also suck in items when they are on partial-sized blocks that sit on the hopper. For example: half slabs, stairs, cauldrons, enchanting table, even a wooden pressure plate(sometimes).
Items on a brewing stand on the hand do not get sucked up, see MC-8864.
Still not fixed, confirmed in 1.5.1.
kumasasa
Can no longer confirm in 14w05b. Anyone else ?
Retested, shows the same behavior as in my original report on 14w05b.
Works as intended. It only looks like it's pulling the item from the web because items visually float above their actual position. The hopper only actually picks up the item when the item is exactly 1 block or less above it.
"Fixing" the "issue" at this point would serve no purpose other than to anger people by breaking their contraptions that rely on this behavior. On a personal level, it would break the ender farm on the server on which I play, as it relies on hoppers being able to pick up ender pearls through soul sand. It would also break the auto chicken cooker that I'm using as it relies on hoppers being able to pick up items through half-slabs.
migrated
The reason for this (I think) is that hoppers in 13w01a were having problems where items that landed on the rim of the hopper weren't getting picked up. In 13w01b, to fix this bug, they increased the item detection range of the hopper. The hopper is probably picking up the item while the item's still in the cobweb because of this detection range increase.