It happened to me after connection to TFS was dropped. and I was moved to offline work mode. Default VSTS settings say whenever you start editing a file it will be automatically checked out and it will appear on Pending Changes window. However, after those connection problems I no longer experienced that behavior.
First of all it’s worth checking VSTS Source Control related settings according to this article. In my case everything was fine there.
The problem on my side was somewhere else. After I had gone offline I had to go online again (what a surprise?!). I was expecting that to happen after reconnecting to TFS, but that is not entirely true. What I had to do as well was use ‘Go online’ button at the top of solution explorer. Once pressed it listed all the files I had modified while in offline mode and VSTS started working as before.