The numbers may be a UI bug. The cyberdeck UI only shows the highest rank quickhack you have for each type. In your case you have at least one copy of all of the legendary quickhacks except Legendary Synapse Burnout and Legendary Detonate Grenade. The other 4 only go up to epic rank.
The only way to tell how many copies you have at uncommon, rare, epic and legendary rank is to go to a buy/sell terminal and manually count them. Its astonishingly bad UI design but it is what it is right now. I assume the numbers in the top right corner are meant to tell players how many duplicates they have looted but I only see zeros too.
Everything to me in your first screenshot looks normal is the same as what I see. In the second screenshot you are not targeting an enemy. You are targeting a device (specifically, an ad stand). You can't use combat quickhacks on devices and never could.