That's expected behavior.

1. you see all cached files, like in the file browser
2. you click on clean (all)
3. Joomla deleted all files
4. you get redirected to the cache view and you see only the files created till joomla does ask the cache what cache files exists
5. joomla creates addition cache entries
6. you reload the page
7. you see the entries created in point 5

the reason you don't have this in the CLI is because you didn't trigger a page redirect (see point 4.)

I'm closing this.