I have a Macbook Pro (Non-Retina) that I use for developing. It's a Macbook Pro 9,1--the last non-Retina model--with a 2.3GHz core i7 and 16 GB of RAM. It has two internal hard drives, as I removed the DVD drive and replaced it with another hard drive. I have Yosemite on one drive and Mountain Lion on the other, so I can test apps I develop on both.

I've noticed a really, really weird thing on Yosemite:

Occasionally, I'll see apps hang with an infinite spinning beachball. I've seen this in Chrome, Adobe Updater, and a few other apps.

If I use Force Quit to force these apps to quit, occasionally the app will quit...but its windows will remain behind! The app doesn't show in the Dock, the task switcher (command-tab), or Activity Monitor. But the windows are still there. The windows can be dragged around but are otherwise nonresponsive.

Occasionally, these phantom, ownerless windows will eventually vanish, after five or ten minutes. Occasionally, they stick around until I restart. I can re-launch the errant app and it works fine, as long as I don't try to interact with any windows that are still hanging around from the force quit.

I am at an utter loss to explain this behavior. Has anyone else seen anything like this?

(Edited to add) I have observed this behavior of a fresh install of the current version of Yosemite.

Do the apps in question all make use of WebKit?

I haven't seen the issue you describe, but I have from time to time noticed individual Safari tab processes persisting in Activity Monitor after having quit Safari. No zombie windows, though.

What I have seen in 10.10.1 is a window that hangs around for several seconds maybe even a minute or two after I have closed an app before it finally gives up and goes away and one app, since deleted, I began to think I was going to have to take a club and beat it to death to get it to quit.

During the Yosemite beta I noticed several apps seemed inordinately slow to close, but whether that was related or not I don't know.

What I have noticed in Webkit is how long it takes after the first window opens for the rest of the app to finally wake up and start functioning. After that the response seems fine.

The app I've noticed this with most frequently is Google Chrome. Older versions used WebKit; newer versions don't. I've also seen it with the Adobe Updater app, which AFAIK doesn't use WebKit at all.