So I've had this happen twice,first time I didn't know exactly why but I went and tested a few theories. It seems if you level up a skill while in 
's passive state, hisQ/R will stop responding period.
I don't know if it extends past Q/R but that's what happened in my experience with this bug.
I have had a bug that if I press 'R' during his passive phase his ult goes on a 142 second cooldown AFTER I rez.
I have also noticed the issue with his Q you listed but I have not had that issue with his R.
I am having the same issue with 's Q and R. By running several tests in custom games, I've realized the action bar and field map respond when these abilities are toggled (sfx + range) but Sion himself with not perform the ability. Also, when attempting to use his Q and R, they will occasionally go into cooldown even though he hasn't performed the ability. W and E respond fine throughout matches; I'll go back to AP Sion 
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