In the Lab Rat comic, The Rattman puts Chell on the list to be the first one that gets to be tested. In portal 2, when wheatley takes over, he puts you through the test chambers GLaDOS made. He also says that it is really easy to put these rooms together. He only has to clean the room of skeletons. But if chell is the first one to be tested, where do these bodies come from?
"Clean out the skeletons" is likely not referring to actual test subjects in this case, but rather the English idiom of "having skeletons in one's closet".
The implication is that he is discovering all these things he didn't know about (or was otherwise repressing his knowledge of) for the first time.
However, it is Portal, so the possibility exists that Wheatley is actually being all too literal. In that case, the skeletons would be from the test subjects (or Aperture Science employees) that GLaDoS killed when she took over the facility. It's important to note that Chell was placed at the top of the "To Be Tested" list, and a list of who to test next gives no indication as to whether or not she was the "first" test subject post-takeover at all.