I need a way for players to get their wands upgraded when they are not holding it.

I am using a different way of progressing in magic.
It uses the wandp add command in command blocks after they press a button to give them a spell,
however, if the player completes the task and presses the button without holding the wand, they miss out on the reward (each challenge can only be completed once, because of permissions). And to monitor this for every players mistake is undoable. Is there a way to add spells to wands without them holding it? They only get the beginner wand and never get another one. Tasks just keep upgrading this one.

7.0 is released, spells and mana can be given directly to players now.

There is probably not going to be a good solution if you're using command blocks, until the 7.0 changes are complete. This will move most wand data to player data.

If your command blocks have some way of tracking when a player has upgraded so they only upgrade once, then you could give them upgrade items instead. These items upgrade their wand when they hold it. However if players can repeat the upgrade and gather multiple items, they can exploit the system by given them to other players.

Unfortunately this is just a limitation of the fact that Magic is item-based for now. 7.0 aims to correct this, but I have no idea when (or even if, at this point) that will be ready.

The only other solution I can think of would involve coding a custom plugin to perform the upgrades.

I have just thought of making it in such a way, that they have to use magic spells to destroy a block that will trigger a redstone effect. As of now it seems to be working perfectly!

it is the only block destructable by worldguard in that region