I only know of one that is still occurring, which is the overall behavior of vertical splitters/mergers.
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Can't snap a lift to them after they're already placed.
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Hard to tell which output is which for smart splitters.
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They vertically snap 1/2 a unit off of global alignment, so connecting belts need to go up or down slightly to realign with the grid.
But they are fixing bugs each update, so I am still holding out hope they'll address that one. For all I know, this one might be a complicated fix for worlds that are already using vertical splitters that could break if adjusted, but a new world state could be the perfect opportunity to force everyone into a "reset" of sorts to make that adjustment.