I am using this 2x hopper speed water stream item filter, but it's missing a significant number of items:
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See in the attached test world: if you pull the lever to turn on the flow of cobble, the filter misses many of them. If you look in the filter hopper, the first slot never hits 64, so seems like it should still be able to pick up items.
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Thank you for taking the time to make a test world to demonstrate your issue. What is happening is not a bug, but rather a limitation of your build. Hoppers have an 8 game tick cooldown after they collect an item entity (stack or partial stack) before they can collect another. The dropper in your world is ejecting cobblestone every 4 game ticks. Most of the items clump together into stacks of 2 or 3 so the interval between stacks going over the hopper is usually 8 game ticks or more, but droppers also give items random momentum and that means the timing or when they proceed through the water stream is not consistent. As a result, some get by while the hopper is in cooldown.
You can work around this by using a gating or grouping mechanism before the item filter. A timed trapdoor or fence gate could be used, or a cobweb. In the example below, the dropper ejects items into a honey block so that they fall into the edge of a waterlogged cobweb at the beginning of the stream. This will batch items in stacks of 14.
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