I tested it with the rc1 3/3 release of nw.js and it still happens for me. I've also heard tale of renaming the project solving the problem, and that doesn't work either.
I export to nw.js to get the executables, and when I run either the Windows 32 or 64 bit versions of nw.exe it happens. I just run the executables directly. I do not close through any internal close function, but close with the X on the window. Having looked around, I've heard a lot of complaining about the issue outside of Construct itself, and I'm reasonably confidant it's an nw.js issue. It appears to create a parent and two children (though I could be mistaken) and when closed it removes the two children, but not the parent. If you run it again it creates three new processes, two of which close when exiting the program, leaving two nw.exe in the process tab. This seems to continue indefinitely. I've put my game up for download and I've seen comments on almost every site related to the game complaining about the issue, so it appears to be a problem with the game files and not just my computer.
It's a bit bloated for an example of the problem, but you can find my game, which does it, here:
http://gamejolt.com/games/tofu-tower/125361