In most cases this duplication is not problematic or even noticeable because minecraft automatically removes the duplicate during load.
However, not so for chests which cause the game to perma-crash due to some weird programming logic that make no sense at all (thanks Mojang!).

About the TileEntity duplication itself: so far no clue why it happens.

Problem found: The Dimensional Block Position instances I was using didn't match properly with regular BlockPos so TileEntities were created multiple times because minecraft didn't find the already existing ones in its BlockPos -> TileEntity map.