Not actually a bug, it was a feature I was not aware of. Please close this, thanks! ****
When a hopper minecart moves off of a powered activator rail, it gets stuck in a locked state and no longer picks up items. This happens when the minecarts moves off of the rail, or when the rail is removed from under the minecart.
HOW TO REPRODUCE:
Place a rail-line with a powered activator rail along it.
Push a hopper minecart across the activator rail.
Throw items on the minecart.
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I see, I never knew that. I had tried pushing it over a powered activator rail to see if that were the case, and when it didn't reactivate the minecart I assumed that's not how it worked. I didn't realize an unpowered rail reactivates it. Good to know, thanks! Should've done more research before reporting this.
This is by design; the activator rail doesn't turn it off, it toggles the fact it can pull in items.