TL;DR: it is rude to save seats and then people show up late to claim them (or don't even show up), but it is just as rude to move other people's property.. "Two rudes don't make a polite". Context really matters: place, people involved, time...
Public spaces, such as bars, concerts, theaters, airports, trains... are full of written or unspoken rules, most of which are just basic behaviours you should have picked up early in your life, as early as kindergarden: just be polite, wait your turn, but the early bird should only gets his worm.1
Many places have policies: theaters, concerts and so on... that non-reserved seats can't be saved, or only be saved for a certain amount of time before the show starts (like 10 minutes), otherwise it's 1st come, 1st served. When facing a claim of "seat saving", in assigned seats or no seat-blocking areas (also known as OPOC: One Person, One Chair, a policy we used to enforce at bars/restaurants I worked for), you either decide to live and let live or go seek out an employee, rather than enforce the rule yourself, which can degenerate into a conflict.
But watch enough people hogging chairs at crowded places and you realize there is no good rule about when you should and shouldn't try to save a seat.
"My friend's in the bathroom." "She's outside having a cigarette." "My husband's parking the car." Then, 20 minutes later, the friend "in the bathroom" inevitably rushes in and sits, wearing a winter coat and apologizing for being late. Fritz Hahn - Washington Post
In some places, saving seats is so common and so accepted a practice that the only real arguments I've heard concerning it have to do with the specifics of etiquette -- how many seats an individual person can save, whether they can be saved after the movie or whatnot has started etc. The etiquette of saving seats for others
Avoid saving seats for people who may or may not show up, or don't have the courtesy to get there on time. Those who are prompt should be rewarded. Reader's Digest -- rules of etiquette that everyone should follow
In your case, you could maybe ask for the seat until she shows up, and explain that you can rest for a while without bothering anyone. Depending on the answer, back to the above lines: do you want to argue, try and enforce your right to have a seat, and escalate or not?
1. inspired by Fritz Hahn - Washington Post