This tends to happen when you are working close to cell borders. Specifically, it occurs when you drop something like a rock into the render window and the cs records that ref as being in one cell then, in placing it you scoot it over the border of the cell into the neighboring cell. So you end up with the record in one cell and the actual object in another. One way to avoid this is to press B when working in the CS to show you where the cell borders are and then, avoid dropping things across cell borders. :nod:
Once you have one, this is not necessarily a bad thing, the messages on load up can be annoying, but in some cases, you can't move the object, you need or want it where it is even though it's causing the error; it's generally okay to leave it. If that's not the case and you can move it, delete it, save, reload your mod and then replace the object in one cell or the other and that should get rid of the error message. The trick is making sure you are deleting the right ref. Some folks have an easier time removing these troublemakers in TES4Edit.
It's perfectly fine to go in game and test while your mod in loaded in the CS. If your rig can handle the multitasking workload, go for it.