I compared the behaviour in Crucial 2 to behaviour in standalone quark w/ oddities. It seems to only be broken with crucial 2.
It's possible that something broke when crates were added but I think it's more likely that multiple mods are conflicting over hopper behaviour or something like that.

Happens because of the waterlogging hoppers feature from Inspirations

Looks like Quark inits the map of block -> behavior on class init, and registry replacement running later results in the map having the wrong hopper block instance.

Fixed by 6f449f9 for now