As an alternative, you can click on the Progress panel in the developer console and click "Cancel All Deployments."
What is going on?
Apex and VF are interesting because they need to be compiled to ensure the saved state of the org is valid. Before, the only way to do this was a deploy in the Metadata API, which requires a ZIP file and a lot more time.
In the Tooling API, a new concept of a Container and Container Members were introduced. Now, these containers can be saved to the org even if they aren't valid. When the user is ready, a Container Deploy Reqeuest is created to deploy that container and all it's members (No more zip file!). This, in general, makes for a much faster save and smaller payloads (instead of one large payload).
The Dev Console has already (mostly) moved over to the Tooling API, and all tools should be moving over eventually. I think Mavens Mate and Brain Engine have already started to use the Tooling API, which is why you may see that error on there too.
There is a restriction where you can't create a deploy request on an entity that is already being deployed (isCheckOnly=false). This helps prevent multiple people from deploying the same object, and overwriting changes. Although, in your case, the developer console most likely got in a weird state where it doesn't think the entity you're trying to save has a member, so it tries to create a new one and deploys that when there is already one on the server. We are constantly trying to make the console more robust to prevent the state from getting out of whack and causing errors like that.