I've been running into this as well, however when I restart the client and server it seems to fix itself. I'm not sure how the deduplication is happening.
EDIT: Leaving the room and then re-entering the room reloaded the construction sites from my local server. Seems like the server does not allow the second site to be added even if the client thinks it was added.
I think I've run into something similar at one point, I don't know when you are trying to access creep object but if you are trying to access memory of a creep that is being spawned, it might not exist in the Game.creeps hash yet. Give Memory.creeps[creepname].role a try and see if it is populated. The new PTR notes have a note about inserting a dummy Creep object into the Game.creeps hash during the createCreep method so it might be fixed in the next version.