Where the pane is narrower than the squeegee blade is long, it is always difficult to achieve perfect results with a single pass. I treat it as 'aim for perfection and clean up any mess with a scrim afterwards.'
Practise will improve results, back in the days when I would squeegee hundreds of Georgian panes with a 6" blade I used to find that first thing in the morning I left lots of marks, but after 20 minutes or so I got my "hand in" and the result was good enough just by squeegeeing without having to polish afterwards.