If a ballot design is determined to have caused a number of people to unintentionally skip a vote on the ballot, are any steps taken to ensure all votes are counted?
No. Ballot design needs to be fixed before the election.
In 1996, it was clear that some people who intended to vote for Bob Dole accidentally voted for a different candidate. This is because the ballot looked something like:
Bill Clinton O
O Ross Perot
Bob Dole O
O Harry Browne
Some people who wanted to vote for Bob Dole, (and seeing that Dole's name was the second name in the left column, which they inferred must have been reserved for major candidates), punched the second mark. So they unintentionally selected Ross Perot, because the ballot's designers counted line numbers, not columns, and Dole was listed on the third line.
Not only did they not fix things so that those people had their votes count as intended, they used the same system in 2000. It blew up spectacularly and they finally fixed it for 2004. Of course, by 2018, they could find a new way to make things not work.
They don't know which ballots belong to which people. If they did, then the vote would not be anonymous. So they can't fix just the bad ballots. To fix things, they would have to redo the entire election. And there is no provision for redoing elections.
The truth is that all this stuff was available before the election. Someone could have observed prior to the election that the ballot was flawed and raised a stink then, when it might have been changed. The system is designed so that once the election happens, there is no way to fix votes. They have to fix things for the next election.