I would bike it over examine each window with pen and paper , if there is 1 bead or a little bit of spotting i would look at all the windows and explain that the clean is satisfactory , considering you have say 10 windows and you have the top left 1x section effected due to your rubber window seals leaking (which i cant help) but looking at the bigger picture i would ask them there and then "are you happy? 1 window has been effected but overall your windows are clean."
its happened to me once or twice they can do nothing but agree with me, they then realize poop , because of one little bead or spot im about to lose my window cleaner and after 4 months my windows will be rotten and they know its hard to find a decent window cleaner who cleans frames too.
WFP is not a magic wand , same way the mop and blade can leave a line or a streak WFP can leave a bead or a spot, i would explain that and i will give it an extra rinse next time and thank them for informing me. As for her not paying its 3% of the glass effected and its no reason not to pay.....
If anything let her give you the chance to correct the fault
say If your Gardiner forgot to pick up a small pile of leaves you would still pay him right
so she should give you the opportunity fix it.
ofc i would go over it if i felt the fault or the finish was not satisfactory.
Good luck thou i know how you feel sometimes its better just to write it off, and move on im sure we have all written off our fair share ,