There are a lot of understudy assignments throughout the cast. The problem may be that they don't have a lot of people who are only understudies...no (few?) offstage people.
So in a lot of cases where they're putting an understudy on, the person who covers the understudy's regular part(s) has to move into that track, so a third person has to take over for the understudy's understudy...even with the principal roles double-covered, once they run through that sequence a few times they start ending up with holes they can't fill. Whether it's that broader coverage would have served them better, or just that there's more illness than they could reasonably cover, who knows.
They could also have more absences than they can fill among the crew backstage...it's not necessarily about having onstage coverage.