This is a know bug on ubis patch notes for the game.....we just have to wait for the patch....it affects a large majority of the people who own the game. (console and pc include) The windmill you rotate cause a desync with your inventory.
A year later and the bug still exists. For those not playing Uplay, the saves aren't encrypted - there are a few 100% saves out there.
But we don't want finished games, do we? NO! We want to be able to finish the damned game we paid for.
Apparently not everyone experiences this bug, So a save file immediately after the three crosses are complete would be all we need. Or a way to trigger the quest to proceed.
One of the crosses which hold the pieces drops under the broken wharf, I wonder if the others also drop into the terrain? Though I can't find a no-clip anywhere either.