Comparators can only read the inventory of minecart chests that are on detector rails.
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Yeah, and it causes some silly problems. Minecart sits on the detector rail so your comparator can read it, and the detector rail outputs redstone signal which blocks the hopper underneath so the minecart won't empty One way around it is to embed two minecarts with hoppers in two blocks under the detector rail. (if you embed just in one, the block gets powered and locks the hopper again...)