Control-clicking a chest on spigot doesn't work (block data isn't copied onto the item), but it does work on vanilla. (I also tested it with the mojang-provided dedicated server software which works as intended)

There are no applicable logs but I attached them anyway.

I placed each control-clicked chest in another chest and took screenshots of "/data get block" which I attached for your convenience (:

(Idk if this helps but the first thing I notice is the spigot server has a "block_entity_data" type and the vanilla one has a "container" type)