The current version of Yank is not designed to support the selective removal of shared files.
Suppose you install ProductA, which creates a file on your hard drive called AlphaFile. Suppose you later install ProductB, later which also requires AlphaFile. The ProductB installer checks your hard drive, notices that AlphaFile is already installed, and therefore does not bother to re-install it. In the future, if you yank ProductA, Yank will remove AlphaFile, not realizing that the file is also used by ProductB. This may result in an invalid ProductB installation. ProductB may be able to recover from this problem by automatically re-installing the needed file, but most programs aren't that intelligent.
Future versions of Yank may have features to help solve this problem. In the meantime, you will have to be aware of it when installing related products. In particular, installing multiple products from the same vendor may land you in the realm of shared files. However, in most cases—for example, when you are download a product from the internet, try it for a few days, and then yank it—you will not run into any shared file problems.
You may find it helpful to search the Yank File Server to see if there are custom Yank files that deal with shared files in precisely the way you require. You may also find it helpful to lock shared files in the Finder to prevent them from being automatically removed by Yank.