he takes his helmet off in the first visit to the temple, pretty sure it is said he lets dripping water fall on his face. Microscopic
viral life-forms could be in said water, which may be related to the black soup of the urns at a more distilled level. If that water gets in his eyes, then he gets eye-worms!
Also bearing in mind for the flow of the film, Shaw has a confrontation with the Engineer and the Big Tendril thing whilst seemingly on the Prometheus, or a possible second ship (Magellan?). If she was fighting the Engineer on the Prometheus, she had to leave and get dirtside somehow to be there when Janek rams the Juggernaut and strands Shaw and Vickers.