I can't really describe why this happened, but I've found two cases of it in a ribbon world I am playing on.
In both cases, the hex only has 7 ports functional; rotating and/or changing the filters does not do anything. Items simply refuse to go in or out of that port. In one case, it was the left side bottom, and the other was a right side top.

That's strange. It sounds like it has something to do with the loader being positioned inside the hex core and perfectly at its edge, so maybe there's some kind of floating point error that causes the game engine to treat the loader as transferring items to and from the hex core's inventory instead of acting as a port. That's just a guess, though. If you enable show-debug-info-in-tooltips in the F4 debug menu and mouse over the loader, is the broken loader's position at a perfect halfway point between tile positions (ending with .500)? And in case that number gets rounded and potentially hides a floating point error, you can also mouse over the loader and run /c game.print(game.player.selected.position.x .. ", " .. game.player.selected.position.y) in the console to see the Lua object's actual position, non-rounded. If either of these display an imperfect midpoint, that'd explain the rare loader bug.

I was able to get the loader to output the console commands above, but it looks like it was at {-37.500, -102.500} and {110.500, -811.500} respectively.
The debug commands simply outputs it as .5 without additional digits, so it looks like those are still correct coordinate-wise.

I have tried to re-generate the map with minimal settings but I cannot seem to get it, even with an identical seed and map exchange seed.
It's possible I might have changed some of the worldgen settings at some point, but it feels like certain parts of the mod are non-deterministic (for example I got a ribbon world to spawn with a dungeon in roughly the right spot, but its shape was different)

I have tried to re-generate the map with minimal settings but I cannot seem to get it, even with an identical seed and map exchange seed.
It's possible I might have changed some of the worldgen settings at some point, but it feels like certain parts of the mod are non-deterministic (for example I got a ribbon world to spawn with a dungeon in roughly the right spot, but its shape was different)

The differently shaped dungeon is likely due to the chunk generation order. That part might not be deterministic, or if it is, it depends heavily on which chunks you visit on your way to see a certain area.