Hopper carts can send items to other hopper carts through blocks. I'm not sure if this is a bug, but if you can pass items between carts with a hopper inbetween, it's quite annoying that they will do it when you don't want them to.
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That might work, but if minecarts with hoppers need to pass over each other, then it's not practical to have activator rails everywhere, especially since that disables the lower hoppers which might be needed.
I wasn't suggesting a solution, I was suggesting a testing method to prove the exact cause of what you experienced. This is probably related to MC-6266.
Ah, ok. But yeah, I feel like they need a smaller threshold for swallowing items or something if that kind of thing is the issue. That and that hoppers don't actually always suck stuff out of carts at all when they're supposed to. But that's probably another issue.
What's most likely happening is that the lower minecart with hopper is sucking items out of the upper minecart with hopper. Try disabling the upper minecart by running it over a powered activator rail – the items should continue to be pulled from the upper cart into the lower one. Conversely, run the lower minecart over a power activator rail, and it should stop.