As others have said, it may well be on the inside, particularly if they are the type of smears that are left behind when large panes are cleaned with a scrim or microfibre cloth.
However.....
If the sun is at the right angle, and it is intense enough, you will see every pass from the squeegee!!
!!
There is ALWAYS, repeat, ALWAYS a residue left behind, but you have to have the right conditions to be able to see it.
Clean the inside of a conservatory where the people who live there smoke (I only use the example of a conservatory because of the high light levels) not even heavy smokers.
you will walk away from the job where the glass may look absolutely pristine, but within a couple of weeks (or a month later) when you look at these windows again the tar and smoke particles will have began settle on the glass and now in almost any kind of lighting you will see every pass you made with the squeegee the month before, every rub of you scrim, every kick of the squeegee you never realised you had at the time....
The residue left behind is sticky and dust and smoke particles will settle on it.
This is not a critisism of anyone, it is a simple fact, get the conditions just right and you will see!!
Things you can do to reduce this effect are to ensure you are using rubbers that are not worn, make sure you have only just enough detergent in your water, the more suds you have in your water the more residue will be left behind.
some of you may well put a healthy dollop of fairy liquid in the water, your squeegee will glide over the glass lovely
But its not good!
If you put your hand in your water and then rub your fingers together and there is a slimy feel to it, then you have WAY TO MUCH detergent in your water!!
So don't beat yourself up over it, it sounds like you have done the job correctly to me...
Ian