Runes setting up in a way we really DON'T want them too

Illogical rune setting system in League of Legends
While setting secondary runes, the rune from the first slot is automatically the one to be replaced even though you clicked on the second slot. If you want to replace a rune from the second slot, you will be doing it twice. What is the logic behind that Riot?
Couldn't find a better board to put this on. It has been very annoying when making changes in the secondary rune tree, the game won't replace the rune you clicked on unless you're switching for a rune from the same "branch". Otherwise, it will always replace the rune from the first slot, even though you clicked on the second slot when making changes. You obviously click on the rune you wanna replace. The current settings are super useless, annoying and lead to playing with wrong runes when you're doing last second changes. Please, Riot, you've finally made runes easy to understand. This is the last flaw to the rune system but it's certainly not a small one. Just for me, it led to multiple games with a wrong secondary rune.
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