Gaping Hole Between Alien and Prometheus

I noticed what seems to be a huge continuity problem between Prometheus and Alien and I was wondering if anyone can explain it away. In Alien, when they find the engineer's suit that in the pilot's seat, his space suit has had it's "chest burst" and it appears that there is no body anywhere inside the suit. However, in Prometheus the Engineer is seen in the suit and he later leaves the suit to chase Dr Shaw around the planet. After their confrontation and his subsequent death he proceeds to have his chest burst by the new Xenomorph outside of the "Engineer's" ship... So my question is, based on the events of Prometheus, why was the Engineer's suit in the pilot's chair in Alien found in a condition like he never left the suit to chase her (Dr Elizabeth Shaw) and instead became infected by the Xenomorph, only to have his chest burst in the chair instead? I hope I'm just missing some small detail, because otherwise this seems too big to miss considering they clearly state that the engineer's suit has had it's chest burst in Alien...