Before the last episode I was fairly convinced that the reason those sent to clean were dying was due to a fast-acting gas in the suit. However, as she was exiting the silo I thought it might have been the decontamination chamber spraying them down with a lethal contact poison that slowly made its way in through poor seals in the suit, but the "good" tape would protect her. Obviously it did, but the problem wasn't decon.
I really enjoyed the show and the ending while dark, is a lot more satisfying than I expected it to be. However, I'm left with questions about how much those in charge really know about the world. Obviously, they know a lot more than the average Joe, but are they even aware that there are other silos just beyond the ridge? I doubt it, because there would be far too much drive to form a larger community for resources, etc.
As someone said, the silos were probably a delicate equation that required total autonomy to succeed and given statistical distributions it's 100% likely that some of them ended up as nothing more than massive tombs.