A lot of confusion here is coming from how the peer bonuses are awarded so I'll give a brief explanation. You can nominate someone for any reason you like but you provide a justification, their manager sees it and decides if they should approve it or not (almost all are approved). Now the important point is the rules state you can't receive more than one peer bonus for a single thing that you do.
It's almost surely the case that 1.) her manager knew that and the other manager didn't or 2.) she had so many pending when her manager saw it that they thought to ask someone what the rules were. For #2 imagine you are her manager and you see 20 people queued up nominating the same person for the same thing, you are responsible for enforcing the rules (in this case giving your report Google's money, it's in the manager's best interest to _approve_ it since their report will be happier) so you don't want to make a mistake and ask around, then someone tells you 'sorry one bonus per thing they do' and you have to deny all of the rest.
I couldn't applaud her more for the salary spreadsheet she put together (it took serious courage) and the really healthy dialog that it brought (I was glued to it when it came out), but the peer bonus part of the story is almost surely not malicious on her manager's part and I hope she hears that somehow. It'd be really sad for everyone involved if this is just a misunderstanding (the peer bonus part at least).