Invisible icons on dock

Yes, you do have an odd situation. I suggest doing a restart in the Safe Mode. Hold down the Shift key at startup. This clears a lot of strange problems. Be patient. It can take up to ten minutes. During the process the OS is clearing its caches, doing various repairs and resetting things. Then look to see if everything is normal or not. Then restart normally and see what you have.

Some further trouble shooting thoughts: Just to clarify, have you tried moving the "offending" icons to the trash and then emptying it? Then, next, dragging the original icon from the applications Folder to the Dock to create a new alias there. You say that you can move the "offending" icons around and open them. When they are moved are they still invisible or is the invisibility only applied to certain locations on the Dock? You might also mention which apps this problem applies to. Last, one thought is that the apps themselves may have somehow become corrupted. If so, reinstalling the apps may resolve the problem.

+1

If the picture you'v shown is what you have, they look normal to me. Am I missing something? If so, please explain the problem with more clarity.

@ Ronasara - +1 Excellent

Glad to hear that. I suggest you keep this in mind. The Safe Mode restart solves all manner of odd problems. It should be our first thing to try.