Something big happened between checking your wife's upgrade availability and you going ahead and attempting to upgrade her.
That big event was: they sold an upgrade (to you, as it happens).
That's a material change that makes them re-assess whether to offer another seat, and if so at what price.
If you really want to upgrade two seats, you really should ensure they are on the same PNR.
Remember that if check in is open it is a highly-dynamic situation and literally hundreds of people will be logging in to check in, many of them seeing similar offers. Each sale - including yours - will have an effect.