Paste to Subfolder in Finder List View
Basically, your way of viewing the folders in the OS means that in the over-arching parent folder that you opened the finder window in will be the folder that it detects you to be in causing your CMD+V to paste into this folder. 

Even if you've expanded sub-folders the OS has made it so that in this viewing format you haven't actually entered the folder so the paste still occurs in the highest parent folder.

Try opening the folder with a double click on the folder name or change your viewing format to columns so checking the contents of folders, like it seems like you want to, is easy but pasting to specific places becomes possible.