Please explain in more detail what you are doing, and posts screenshots if needed. Lightroom's folders are the same as the folders on disk, but Lightroom also has collections, which is something else. For example: If you drag an image from the Recent Imports into a folder, then that image will be moved to this folder, but it will remain in the Recent Imports. That's because Recent Imports is not a folder, but a collection.
Johan, you might not believe this, but I have never used Collections. I know it is a very powerful tool. I remember when I first started using LR well over a decade ago, Clete and Jim and even Victoria were telling me to start using them and not rely so much on my traditional folder structure in terms of how I work with and view the images. But even after all these years, I still organize everything as folders, probably because I am a travel photographer and name folders after the trips I go on, or if it is a specific shoot I do at home, I just name it some way that makes sense. I never name folders or files with dates, as I know many daily shooting pros do (and for good reason).
I have one folder called pictures. I have one LR catalog. In that folder are literally thousands of folders and sub-folders, and each image in those folders is file and title-named in a way that makes sense to me or would even make sense to a new observer of the folder tree.
When I edit my raw files in LR, I always apply Titles, Captions and Key Words to each image. That is a lot of work, but I always do it. Therefore, if I wanted to, I could make a Collection of anything very easily. I just have never wanted to. For example, if I want to see some Rome shots, I just go to one of the many Rome folders since I have been there so many times and shot it since 1984 (and as recently as two months ago).
If I wanted a Rome Collection, and it grabbed every image that has Rome as a Key Word, it would be a collection of many thousands of raw files and TIFF files (scanned slides and negatives) shot over many decades.
I know Collections are a powerful tool. I just have never use that tool. Wait, I did use it once. Someone wanted me to send them some images shot with a particular Fuji GF lens (I have them all) for a review for a publication. So, I went into my Raw file folder and told LR to make a collection of every image shot with the 23 MM GFX. In seconds I had a thousand 23mm GF Lens images in a collection taken from hundreds of different folders. Pretty powerful.