At the end of the exhaust stroke, not only does the piston start moving back down the bore to ingest the fresh mixture, but the intake valve also opens to expose the fresh air charge to this event. In modern automotive 4 stroke engines valve overlap occurs at all RPM, so for a short period of time the exhaust system is open to these low pressure influences which can suck things back towards the cylinder. if the exhaust gas velocity is low and pressure is high in the system, this will make everything turn around and go the opposite direction it's supposed to.
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