bellanrocco, maybe it is time to get the apartment manager to get the pest control folk up to check your apartment.
I did see other Yorkytalk members,(I apologize I forgot your names) suggest the critter connection.
It is true that Yorkies are able to find rodents and your's is a young dog and maybe even interested in barking at spiders or bugs. Not saying that your apartment is infested, no, but the way buildings are made and creatures of all manners can get into buildings and do on a regular basis. Mice, bugs and snakes can crawl around inside the walls without our knowing it, but the dogs can hear them. I am sure that you are doing nothing wrong, but there is not a building made that creepy crawlies can't get into!
As an example, the following is definitely not your problem, but it shows that critters who want to get in, can and will what ever way possible!
I saw a tv news crew report on some poor woman in Winston Salem,N.C. who had rats swimming up through her toilet and had the tv crew there with cameras to prove it. A plummer then told them how to fix the problem with a different valve to prevent the critters from being able to get in.
We used to have a neighbor up the street who's dog barked at a plastic bag that had blown against the fence. It did not belong there and had gotten there under its own power and should leave, as far as the dog was concerned
My dog barks when our outside cat wants to play and dosn't matter to her that it is 2 or 3 am and 17 degrees F out......
Sitting with her and calming her when she does this, probably only encourages her to continue to do this and causes problems for anyone trying to sleep when she does bark at odd times, or for you because it alarms you and you're not sure what she is alerting to. So for the most part you need to ignore her when she does this or distract her but don't "condone" it by sitting with her and petting her, it makes her feel she should do it again, when you encourage her to do so by "calming her" afterwards. This may take a very long time and lots and lots of patience on your part.
Good luck!