Had similar problem. Files were donwloaded in 'Downloads' but when right-clicking on 'Show in Folder' it showed the Desktop.
I did the following to make it work as normal.
In Chrome, go to Preferences, then go to the bottom and click on Advanced, then go to the Download section.
Double check if the path is correct. (if not, then that might have been your problem).
Then set the 'Ask where to save each file before downloading' on On
Go to a website and download and image or go to your Webmail and download an attachment.
Save the file to the right folder (in my case 'Downloads')
Then go back to the settings and set the 'Ask where to save each file before downloading' back to Off
Then the first will still go wrong, but the second and following times it will download it in the correct folder.
- macOS Mojave 10.14
- Chrome Version 74.0.3729.169 (Official Build) (64-bit)