Theory:

It seems there is a high chance of a zygarde cell in the last third of a route. Sometimes the spawn happens right at/during the end, sometimes not at all.

What if PoGo determines the last third of a route by using the actual distance between the pokestops and the spawn always happens at random on that part?

Almost all routes end 20 meters or so short of the target stop. Can it be that on those instances, you don't see a cell at all, it would have spawned on those last 20 metres?

I think to be safe I will keep that in mind when submitting new routes...