I see I'm not alone. I made a quick booking for RTE-NYP on Friday, for travel on Saturday. Same thing - got the tickets emailed, had the trip show up in the app, able to change seats, and it scanned properly - no problems on board. But as of Monday, still no points deduction from my account. Meanwhile, the return trip on Sunday (booked immediately after - did them separately as one-ways) deducted quickly, and immediately added the credit card rebate back.

I'm guessing they'll eventually discover the points were never deducted, but at least in my case, the ticket was valid and no problem on board.