I don't think there's anything to fix. What if the files are on an external disk that you have not connected? If MC doesn't find the files, should it delete them from the library? Absolutely not! If you reconnect the external drive and find all your beautifully tagged media missing from MC15, you would not be happy. We cannot expect a piece of software to read our minds, at least all the time.
MC is library based; if a corresponding file isn't found, MC will let you know, but won't delete the entry.
This is actually a great feature for me. I have a copy of my library with me at work, without any of the files. This allows me to check what I have in my library at home at any time. Sure, all the cover art shows the yellow cross, but at least I can check whether I bought that copy of Shawshank Redemption- before I jump on a special offer and inadvertently buy it again online.
What you should consider the next time you delete files is to do it within MC... if you want MC to know about it.