I noticed some time ago that a few hopper minecarts are missing in my melonfarm. After some investigation i found some warnings:
[11:06:10] [Server thread/WARN]: Can't keep up! Is the server overloaded? Running 2040ms or 40 ticks behind [11:06:17] [Server thread/WARN]: Wrong location! (-13, -44) should be (-13, -43), apk['Trichterlore'/36455, l='SSW', x=-199.51, y=72.57, z=-688.50] [11:06:17] [Server thread/WARN]: Tried to add entity minecraft:hopper_minecart but it was marked as removed already [11:06:20] [Server thread/WARN]: litetex moved wrongly! [11:06:35] [main/WARN]: Received passengers for unknown entity
[20:19:58] [Server thread/WARN]: Wrong location! (-15, -45) should be (-14, -45), aml['Melon Slice'/19269, l='SSW', x=-227.64, y=72.39, z=-704.26] [20:19:58] [Server thread/WARN]: Tried to add entity minecraft:item but it was marked as removed already
It seems like if the entity has an unexpected position it gets completely removed.
Please look at the logs for more details.