Dock Folders Displaying Duplicate and Deleted Files

I added the Downloads and Application Folder to the dock.

Recently the folders in the dock started to display files and folders that i had already deleted. Additionally there are multiple entries for the same file/folder. These start to pop up randomly. Changing the view (List/Grid/etc) makes no difference.

I can only get rid of these ghost entries if i remove the folder from the dock and add it again. But this is only a temporary solution as these entries start to reappear over time.

If i click on these ghost entries nothing happens. This is really annoying because i never know which of the duplicate entries is the real one.

I have added a screenshot to help you understand the problem.

How can i fix this?