MCEdit will move blocks, but sometimes not move the TileEntities associated with the object, causing the TileEntity and the corresponding object to be stored in different region files, which makes Minecraft (understandably) complain. This is a nuissance, because it spams the console with "wrong location" messages, which look like AutoReferee causing problems (even though it is not). These problems can be fixed, but it requires some NBT twiddling that is, quite frankly, a massive pain.

Either this fix needs to be automated in the saving process, or users need to be told that there is a problem and pointed to a means of fixing it. This problem is entirely non-trivial.

For reference, these look like:

2013-08-06 19:09:40 [WARNING] Wrong location for EntityItemFrame['entity.ItemFrame.name'/2172722, l='world-autoref-140568968a8', x=-1.94, y=74.50, z=467.50] in world 'world-autoref-140568968a8'!
2013-08-06 19:09:40 [WARNING] Entity is at -1.9375,467.5 (chunk -1,29) but was stored in chunk -5,-12
2013-08-06 19:09:40 [WARNING] Wrong location for EntityItemFrame['entity.ItemFrame.name'/2172723, l='world-autoref-140568968a8', x=-1.94, y=74.50, z=466.50] in world 'world-autoref-140568968a8'!
2013-08-06 19:09:40 [WARNING] Entity is at -1.9375,466.5 (chunk -1,29) but was stored in chunk -5,-12