Folders, Items in folders that don't belong there

Why are documents and downloads showing up in folders that I didn't put them in? For example, I created a smart folder for my brother's genealogy information a couple of years ago, I am organizing my folders and click on his folder and it has 1329 items in it from auto statements to medical documents, recipe's, system information, etc. What gives? I didn't put those items in there, how did they end up in his folder? I find it hard to organize my files when this is happening! Any ideas? Thanks