I had that happen first day I upgraded to Windows 8.1, at first the apps looked fine when it first started up, then I installed Avast 2014 Final release, restarted, came back with a bunch of Down arrows on the apps, (Still have them on Admin account, haven’t bothered fixing those yet) as i’m usually in my Limited User account to do everything

Prior to installing 8.1 I removed Avast 9.0 beta RC3 the following way

Uninstall thru Add/Remove Programs on 8.0
Restart to safe mode
ran aswclear
restart to regular mode
used rezors uninstall utility

Proceeded with 8.1 upgrade, Got updated video drivers in, Avast 2014 final, (restart), down arrows on every Metro UI app, Windows updates, down arrows remained, uninstalled Megatube, Down arrows went away, reinstalled Megatube, down arrows returned briefly, fixed by excluding Megatube in Deepscreen with Avast, then haven’t had down arrow issue since

Reinstalling the Apps did fix it

Happens I heard when app doesn’t sync right or Avast blocks an app with Deepscreen, did that for me on MegaTube) once I removed Megatube and reinstalled it, all the down arrows went away