Or the third variable problem of other variables that could cause both. For example poverty can cause longer commutes and divorce.
Or a mediator problem. The impact is not really Commute -> Divorce but Commute -> Stress -> Divorce. They did cite that "Previous work has found that 45 minutes is more or less the threshold at which the maladaptive side of commuting presents itself with increased vigor." So that means there are several confounding factors. This seems especially apparent given "When people commuting a long way for a long time — in this case, more than five years — their relationships actually proved much stronger...some people may simply acclimate better than others to a long trip into the office."