There were a number of counties with scan ballots where voters both voted for Al Gore and then wrote Al Gore's name in. These votes were rejected but should have been counted for Gore. Gore would have won with these votes.
I am active on voter protection issues and I have posted articles on the recount. I could not find my posts but I did find this from the editors of DU from 2001
https://www.democraticunderground.com/articles/01/11/p/12_gorewon.html
As the National Opinion Research Council (NORC) Florida recount results hit the press last night, one thing is clear: Not only did more people nationwide choose Al Gore as their President, but more people in Florida cast their ballots for Gore.
A year after election day, we have bittersweet vindication that a statewide recount — by any standard — would have handed Gore the state, and the presidency. Whether you like your chads dimpled, hanging, or poked clean through, Gore is your man.
The final numbers? Gore by a margin of 60 to 171 votes (depending on the standard) had every legally-cast vote in the state been counted. This may not seem like much, but it's plenty. In a Democracy, the idea is that the majority decides who will represent them. Gore's margin is small, but it still puts him on top.
Keep in mind that the NORC totals do not include a huge number of additional overvotes that favored Gore by a large margin. From the New York Times: "More than 113,000 voters cast ballots for two or more presidential candidates. Of those, 75,000 chose Mr. Gore and a minor candidate; 29,000 chose Mr. Bush and a minor candidate. Because there was no clear indication of what the voters intended, those numbers were not included in the consortium's final tabulations." But even without this relatively huge block of votes, Gore won Florida if the recount had been allowed to proceed.
Not surprisingly, the conservative news media seems to be giving the greatest amount of play to the revelation that Gore's flawed recount strategy would have resulted in a Bush win. But this angle misses the point. The point of the recount was not to weigh the merits of Gore's strategy. The point of the NORC recount was to determine once and for all who really won Florida.
On that, the recount leaves little doubt; Gore won.
See also
https://www.cnn.com/2015/10/31/politics/bush-gore-2000-election-results-studies
The studies also show that Gore likely would have won a statewide recount of all undervotes and overvotes, which are ballots that included multiple votes for president and were thus not counted at all. However, his legal team never pursued this action.
Again, scan ballots were new in 2000 and evidently a good number of voters checked the box for Al Gore and then wrote Al Gore in on the ballot which caused an "overvote" which invalidated the ballot. If these ballots were counted Al Gore would have won
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