Absolutely, and several of them were carried by Bush.  During the first statewide recount, at least 9 or 10 counties manually canvassed returns rejected by machines using the statutory "intent of the voter" standard.  These include Seminole, Polk, Orange, Gasden, Lafayette, Hamilton, Franklin, Taylor, and Washington.  In some cases, these counties counted overvotes, in some cases they canvassed overvotes, and in some cases they canvassed both.  There justification for these manual reviews can be found in Section 101.5614(5), which states: "If any paper ballot is damaged or defective so that it cannot be counted properly by the automatic tabulating equipment, the ballot shall be counted manually at  the counting center by the canvassing board....No vote shall be declared invalid or void if there is a clear indication of the intent of the voter as determined by the canvassing board."

A quick overview of quotes from various news sources confirms these accounts.  Based on Bush's argument before the Supreme Court, Florida's entire vote tally violates the constitutional equal protection standard because not every county conducted a manual recount and those that did used varying interpretations of what constituted a clear indication of voter intent.
 

Orange County  (http://orlandosentinel.com/automagic/news/2000-11-10/ASECelrecount1111000.html)
Most of the "new" votes in Orange came from ballots that simply weren`t counted Tuesday night, mostly because the machines
couldn`t or wouldn`t read them.
 

Seminole County  (http://orlandosentinel.com/elections/1110sem.htm)
The margin preserved Bush’s tenuous hold on Florida, giving him a 327-vote lead in an unofficial tabulation of the recounts in
all of Florida's 67 counties. The process is far from over, however. Democratic officials have demanded manual recounts --
such as the type that took place in Seminole -- in four counties, including Volusia.
 

Polk County (http://www.theledger.com/local/elections/12pore.htm)
Some ballots were improperly marked and had to be examined by the canvassing board. Some voters marked the oval on the
ballot but didn't darken it enough to be counted. Some voters wrote in the name of Bush or Gore in addition to darkening the
oval.  Those ballots would have been considered invalid by  the machine on the first count. But many were counted
Saturday and added to the candidate totals.

Under Florida law, a canvassing board is to determine  the intent of a voter where that is clear and award the vote.

Each of the Polk ballots in question were examined by Republican and Democratic party monitors, who got to look but not
touch.
 

Gasden County (http://www.nytimes.com/2000/11/11/politics/11REPU.html)
But in Gadsden County, the canvassing board decided to  examine 2,124 ballots that had been rejected by a counting
machine because more than one candidate had been chosen on each. Here, as in a handful of other counties, voters marked
paper ballots with a pencil. The canvassing board did not examine the rejected ballots on election night.

The next day, when they sorted the rejected ballots, the canvassing board counted 188 new votes: 170 for Mr. Gore,
17 for Mr. Bush, and 1 for a local write-in candidate.

Members of the canvassing board insisted they had complied with Florida law. They said they had only counted
those ballots on which the intent of the voter was absolutely clear.

"We were trying to determine the intent of the voters," said Judge Richard L. Hood, the chairman of the canvassing board
and a Republican. "As far as I was concerned, the election was fair."

Sterling Watson, a county commissioner who helped conduct the recount, said the canvassing board used common
sense.... In some cases, Mr. Watson said, voters had filled out the circle beside the name of one candidate, then crossed
it out and filled in the circle for another candidate.

"We made a judgment that somebody made a mistake and corrected their mistake, that's all," Mr. Watson said. He
said  officials followed the same practice for the primaries.
 

Various Counties (http://www.nytimes.com/2000/11/16/politics/16HAND.html)

Limited hand-counting did take place in at least some of the seven counties Democrats cited: Franklin, Gadsden, Hamilton,
Lafayette, Seminole, Taylor and Washington. In some of the cases, election officials counted by hand only the ballots that
counting machines had rejected, usually a small percentage of the total. The hand counts were done not necessarily at the
request of the Republicans, but as part of the county's vote-counting procedures.

In six of the the seven counties, the Republicans picked up votes. But the Democrats also picked up votes, and in one
case, they picked up far more.

A similar hand count was conducted in Lafayette County in northern Florida. Though nearly 90 percent of the county's
4,040 registered voters are Democrats, the county voted overwhelmingly for Mr. Bush.

Officials tried to decipher some 220 ballots the machine had rejected. Lana Morgan, the county supervisor of elections, said
officials were able to determine the voters' choices on about 50 of 220 rejected ballots. In an interview today, Ms. Morgan
said no one kept track of how many of those votes were for Mr. Bush or Mr. Gore.
 

Various Counties (http://www.salon.com/politics/feature/2000/11/28/hand/index.html)

In Republican Seminole County -- where local Democrats are suing because Republican election officials allowed GOP party
volunteers to correct absentee ballot applications that had been filled out improperly -- the canvassing board decided to
manually examine unreadable ballots during the county's electronic recount. Seminole's recount yielded an additional 98 votes
for Bush.

A similar procedure was followed in Polk County, where a partial manual recount resulted in Gore losing 90 votes that had
apparently been counted twice. Canvassing board member Bruce Parker classified his county's actions as "a mini hand
count."

In Taylor County, where Bush picked up four votes, Supervisor of Elections Molly Lilliot said all ballots were re-fed
through the tabulating machine for the recount. "All ballots kicked out were examined individually by the canvassing board," she
said.

"We ran all the ballots back through the machine," said Carol Tolle, supervisor of elections in Hamilton County. "Every time
you had an overvote or undervote, we inspected it. If we could determine the intent of the voter, we counted those votes." In
Hamilton, Gore ended up picking up seven votes.
 

Polk County  (http://abcnews.go.com/sections/politics/DailyNews/florida_election_recount_001116.html)
A similar sort of review benefited Bush in the more  Republican Polk County, where Bush appeared to post his largest gain
over Gore in a Florida recount, 108 votes.  Canvassers discovered some voters had improperly voted twice on some of their
ballots by both voting for their candidate, Gore or Bush, and writing-in that candidate’s name, says Polk elections Vi
Thornburg.  The vote reading machines had rejected those votes altogether, spitting the ballots out into a special container.
Since those voters clearly wanted to vote for just one candidate, canvassers added the votes to the candidates’ tallies, one per
voter, with more ultimately going to Bush, she says.