I have similar problem. Seems to be new UAL.BOMB.

Sponsored companion upgrade with CR1 but did not succeed (Jan 17) - upgrade did not make it back to my E-Upgrade Summary but when I recently upgraded one of my own flights the available CR1 upgrades total on that screen was one greater than shown in the summary!

Unfortunately the 'invisible' CR1 was not applied to my new itinery. I am hoping that this thread may help in getting this programming problem resolved!