OS X Dock wont let me remove icons
Have you checked if your Dock is maybe locked? You could try out the following command in the Terminal app:
defaults write com.apple.dock contents-immutable -bool false
(the above command unlocks the dock)
Then force-quit and restart the dock by typing:
killall Dock
Then try to right-click (or CMD click) on the question marks in the dock, and under "options", choose to remove them.
Hopefully this helps... if not I'll do some more digging for you.
Source: https://forums.macrumors.com/threads/unable-to-remove-greyed-out-question-marks-in-dock.1701440/post-18705823