Your administrator seems to be complaining about three different things:
1) when you ask her to plan travel at the last minute, you risk not getting flights and hotel space, because lots of planes and places are sold out;
2) when you ask her to plan travel at the last minute, you make her job harder and she doesn't like it;
3) you should subordinate your convenience and your clients' needs to the convenience and needs of airlines and hotels.

IMHO point 1 is fair to remind you of. (And you know it already, as we all do.) Point 2 may mean that she sometimes forgets that your organization (like mine) is here to make money by serving clients, including clients who wait until the last minute, and her job (and yours) is to serve those clients profitably, including last minute travel. I don't understand why she would say or imply point 3 unless your primary clients are the hotels and airlines with whom she has to book your travel.

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"If you want to win the game, write the rules."