El Capitan: You can't open the application 'app name' because it may be damaged or incomplete

Ran into this multiple times. After initially upgrading to El Capitan 10.11.2, after logging into my main (admin) account, I could not open any applications, and received the following error:

"You can't open the application 'app name' because it may be damaged or incomplete."

I could not open "Activity Monitor", "System Preferences", "Finder", or anything (either system provided, App Store, or other). The icons would revert to the default application icon. Other users had no problem with the same apps.

After freaking out, I found a solution: go to another admin account, delete the old user account, and re-add it. This fixes the problem for that user; it apparently rebuilds the user identity information for that user, while leaving their home folder (and preferences, documents, keychain, etc) alone. iCloud information has to be re-entered, but it's trivial. After the user delete and re-add, I was able to run those applications.

When I upgraded to 10.11.3, the same thing happened, but to 3 accounts. I was able to fix this via the Guest account - i.e. I was still able to authenticate as an admin, but I couldn't login and run anything.

El Capitan removed permissions repair; I believe it can be done at the recovery console, but I shouldn't have to do that.

Any idea why this keeps happening?

Searching for the above error message usually is specific to App Store applications or other applications, not to things like "Activity Monitor" and "System Preferences".