Which app(s) have the question mark(s) in the Dock? Are you sure you have the latest version of each of those apps installed ... and that you had the latest version BEFORE the OS upgrade?

Can you launch the apps by clicking on them directly in your Applications folder? If that's the case, then the simplest thing will be to drag the old placeholder question mark out of the Dock and drag the current, working one in. You can either drag it directly from the Applications folder (it won't move the actual path to the app, just create a path from the Dock), or else when the app is running, click and hold its icon in the Dock until a pop-up menu comes up above it (again, something that as far as I can tell you have to physically click the button), then from the Options submenu, check "Keep in Dock." Then you can drag the icon to wherever you want it in the Dock.

If you can't launch the apps from their icons in your Applications folder, if you restored from a backup, it's possible that you excluded your apps from the backup protocol when you set it up, so you will have to download and re-install fresh copies. That's really best practice anyway.

What browser are you using?