Remember that it took Clinton months and months (and months) to acknowledge the obvious — that she needed to apologize for the whole situation (even if she, in her heart of hearts, believed she had nothing to apologize for). She eventually did just that in an interview with ABC's David Muir in September; the next few months, whether by coincidence or because of that apology, were the best of her campaign.
But it's clear from Clinton's response to Cuomo's prodding on Monday night that she simply doesn't really understand why the issue is still a problem for her — in the primary fight against Sanders and/or the general election race. When asked whether she should have apologized sooner, Clinton responded: "I had no intention of doing anything other than having a convenient way of communicating, and it turned out not to be so convenient. So again, we’ve answered every question and we will continue to do so."
Then she went to her too-legalistic-sounding pat response of the months before the apology — and, in so doing, might have made things worse from a political perspective. "I’m not willing to say it was an error in judgment because what — nothing that I did was wrong," Clinton told Cuomo. "It was not — it was not in any way prohibited."
That, of course, is a legal point, not a political one. Clinton continues to not grasp the difference. Legal arguments work in a court of law. This campaign is being fought in the court of public opinion. The same rules simply don't apply.
Imagine this: A TV ad featuring video of Clinton's insistence that "nothing I did was wrong" overlaid with news reports about the number of classified and top-secret messages found on her private server. Now, that might not prove that Clinton was incorrect when she said that she never sent or received any emails marked classified at the time. But, man oh man, does it help drive the narrative that she bent the rules —because, well, she could.
It is, of course, possible that sometime soon the FBI investigation, of which Clinton is not reportedly a target, will turn out to be a giant nothing-burger — a move that would significantly defuse the energy around the issue. (Conservative Republicans would almost certainly still believe that she had done something wrong, but the issue would probably lose salience for the ideological middle of the country.)
As long as there is uncertainty surrounding that investigation, however, Clinton's inability to develop an effective two- or three-sentence response to questions about her emails will haunt her — and provide fodder for Republicans in the general election.