I've had this happen also. This is what seems to happen.
When you are on a screen, only a certain number of squares/tiles around you are updated with object information. In the case of houses, if part of the house is place on squares/tiles that are within the update range, the whole house will be loaded into memory, though it may not all be shone.
I'm not sure if the house needs to have been completely shown or updated or not. However, when you log out with part of a house within the square/tile update range and part outside, it seems like it doesn't erase the memory of the house data that is outside the square/tile update range.
The times I've noticed 'ghost' houses, they have only been partial houses. It isn't noticable when you are at your house because it lines up perfectly with the houses there. However, when you go to another facet, the partial house data, that wasn't within the square/tile update range at the time of last log out, can appear.
It is really easy to find with Trammel/Felucca because the house location relates to the same place on both facets. Other facets are a little trickier to find, so they might not be as apparent.