In a conversation with Mrs. Grose about how to handle children, the governess metaphorically presents bad behavior as some sort of contaminant, as if it's infectious and has the power to corrupt others:
"You like them with the spirit to be naughty?" Then, keeping pace with her answer, "So do I!" I eagerly brought out. "But not to the degree to contaminate—"
"To contaminate?"—my big word left her at a loss. I explained it. "To corrupt."
She stared, taking my meaning in; but it produced in her an odd laugh. "Are you afraid he'll corrupt you?"
The metaphorical idea here is that bad behavior is contagious and has a very tangible impact on other people. This highlights the governess's fear that she might not be up to the task of caring for Miles and Flora. It also hints at her growing—but as of yet unarticulated—fear that there's something wrong with the children and that there's a reason nobody else has agreed to educate them since their last governess died.
By the end of the book, though, it's not all that clear whether the children "contaminate" the governess or if it's perhaps the other way around. Though the governess is terrorized by the idea that the children are in cahoots with the ghosts, it's possible that she has deluded herself and, in doing so, has ultimately "contaminated" the children with her fear. In this reading, the metaphorical idea of contamination is especially relevant, as Miles ends up dying under ambiguous circumstances—in keeping with the metaphor of contamination, it's arguable that he has been fatally infected by the governess's fear. If this is the case, then it's a good example of situational irony: the governess, who originally worried Miles might "contaminat[e]" her with his bad behavior, ends up "contaminat[ing]" him with her fears and anxieties.
