At present, in trying to tidy up and organise documents by moving selections of files and folders between Libraries, you are playing a guessing game:
- sometimes it works
- sometimes you get the message 'moving to other places? If you don't see the destination you want below, try moving fewer items at a time'
And then you have to play a guessing game, exploring every folder and subfolder one-by-one, losing your existing selection

This makes tidying up any volume of folders an absolutely total nightmare.

Either let the files be moved, or specify where the problem lies.

SharePoint is simply not fit for purpose as a data/document management tool while files cannot be freely moved.