When you're dealing with a somewhat dense pen of animals, opening the gate to auto shoo causes the animals to get out of the way which is really useful. What is a pain though is when one of the auto-shooed animals hits another animal fairly close by and stops. For some reason this tends to trigger them to engage in wandering behaviour. And due to how that's coded (I'm hunching that it picks any pathable spot within X radius?) there's a solid 50/50 chance they path straight past you out the gate you just opened.
If the auto shoo disabled wandering behaviour for a short time (5s?) this wouldn't happen in the majority of cases.