Important Rune Page Bug with runes specifically.

So say I am on the the Beta Client, putting runes into one of my rune pages. SoI have (Tier 3 for both) 9 magic resist runes and 4 scaling cooldown reduction runes. I put 6 magic resist runes in and 3 scaling cooldown reduction runes in. Then I decide to change the run page to a different champ. So I clear all of it, but I only get back 6 magic resist runes and 3 scaling cooldown reduction runes. The original 9 magic resist runes and 4 SCR runes have been reduced to 6 magic resist runes and 3 SCR runes. So I go into the store and check how many Magic resist runes I have bought. It says I have bought the max amount which is 9. I haven't bought all the SCR runes so I can still buy them but says I have 4 already. So I have missing runes, this also applies to any other runes I put in an amount that was less than 9. So if you could please help me figure out how I can fix this it would be great. Also, if one of the solutions is to go to the legacy Client, I already posted a discussion (on Report a Bug) named "Bug Launching Legacy Client". That entails why I can't access the Legacy Client.