As far as I can tell the backups are stored under ~/Library/Application Support/MobileSync/Backup/ (or somewhere else depending on your OS version). That appears to be somewhere within the applications storage 'area' of the drive, which does make sense as Apple likes to keep all files related to certain applications within app-specific containers. Because of this, the files produced by backing up your phone are counted towards the 'applications' total.
The 'manage storage' dialog is meant to provide an overview that enables you to quickly identify areas that could benefit from cleaning up. The list presented there is not meant to be a complete overview nor do the categories promise to be 'exclusive'. I see how this can lead to puzzles like this, but I do not think that this is a bug. If you want a more complete overview of what's stored where on your drive, there are other third party apps that can deliver that. Personally, I don't bother with this. I too back up my phone to my MacBook but have never seen this as an issue. It probably explains my 80+ Gb value for 'applications' but the more important issue is whether your total storage has enough free space. As long as you've got enough room to play on your drive, I would just back up your phone as normal and only keep an eye on the total storage in use.
Just curious, did the change in the size of the empty space reflect a single instance of those backup files?