Ideally this would have been established beforehand
I've played with new GMs before and these situations can be tricky, and even more so with certain personality or relationship dynamics at the table. It's helpful to establish beforehand a method to address concerns so all players, including the GM, feel comfortable. At a new GM table (and at any table) I ask on the first day of the group meeting how the GM would like the players to address rule concerns. Let the GM guide you on what works best for them.
It's not too late
Just because you've started playing without establishing how to address concerns it doesn't mean you can't still do it. Until you do, let this specific situation lie. It's more important that you establish clear lines of communication that everyone is comfortable with than rushing into solving this specific problem. It's much easier to fix some misappropriated XP than bad feelings at the table.
At your next meeting when you're all at the table, but before game play, ask the GM how she would like the players to address any concerns they have. Listen to what she says and then take her lead. (She may also need time to do research or consider what would actually work best, in this case give the GM the time she needs to figure it out.)
It's worth noting that a new GM may not know what would work best for them, or the group, here. So be flexible if they decide to change it up later down the road.
Learning to GM takes time. There are a lot of rules, and there's a lot to manage. Even experienced GMs slip and need to be corrected. Like any new player, a new GM needs an enjoyable first experience to build confidence and appreciation for the game. Any time a concern comes up ask yourself, "is this so important that it affects my level of enjoyment at the table?"
If it doesn't affect the level of enjoyment and it's just rules for the sake of rules, let it lie. I have found that when I let go of my sometimes rigid expectations around rules the game opens up in new ways and can be more fun than I ever imagined. If it does affect the level of enjoyment address the concern using the method established by the GM.