I encountered the same issue with the reservations being 'out of synch'. I am booked on FAI-ANC-ORD-CVG in August and applied 20 PP for the ANC-ORD leg but, after a schedule change, I was moved to the nonstop FAI-ORD leg. I am meeting someone in ANC so I switched back to my old routing and, forgetting that I already applied PP, I applied 20 PP again for the new ANC-ORD leg. The result was that I was waitlisted on both FAI-ORD and ANC-ORD and 40 PP were 'requested'. I wasn't able to cancel the upgrade requests on either leg so I spoke with an agent who cancelled them for me and then told me she reapplied 20 PP on ANC-ORD as I wanted.

Strangely after all that, now I see 20 PP gone from my balance and I am no longer 'waitlisted' on the ANC-ORD leg (still in Y and on the UG list because of CPU). When I navigate to 'My Trips' it shows 0 PP deducted. However, when I go to 'Activity'>'PlusPoints upgrade activity' it says "PlusPoints Upgrade Redemption (anc-ord)" with -20 points deducted. Any ideas on what is going on here? Do I need to call again?