It's not guaranteed to cause a problem if it's programmed exactly how it needs to be, but because of that, it's not considered a good practice.
You can get flickering outputs if rungs aren't arranged exactly correct as far as the scan order is concerned. We have several SLC programs running here in the shop with duplicate destructives (multiple of the same outputs) that don't cause issues, but it gives me a facial tick whenever I have to work on those programs.