Photos and video from late in the parade show a clearly damaged trophy hoisted by Red Sox players.
However, a photo from before the parade shows all four trophies carried on the ducks intact.
"The damage was minimal and nothing that can't easily be repaired," Red Sox spokeswoman Zineb Curran said in a statement sent to WFXT later in the day.
Security was heavy for Wednesday's duck boat parade carrying the victorious Red Sox through downtown. Police reported at least six arrests. One man reportedly tossed a full can of beer at one of the boats, and it struck and slightly damaged a World Series trophy.
Video captured by WFXT along the route shows players in an orange duck boat looking concerned and pulling a trophy inside the boat.
This was captured moments after several beer cans flew toward the duck boat.
But the obviously bent flag pole on the trophy may have been a side effect of the way some players appeared to be holding it.
Hundreds of thousands of jubilant fans skipped school and work to cheer for the team, giving this year's Halloween a special flavor on a crisp autumn day. Many wore Red Sox gear instead of Halloween costumes.
The Sox defeated the Los Angeles Dodgers in Game 5 on Sunday to bring another championship home.
Members of the World Series championship Red Sox were taking turns hoisting the trophy, triggering deafening cheers from adoring fans.
Some fans, however, were a little too generous with flying cans as several people in the parade said they were hit with beer cans.
WFXT was told Red Sox manager Alex Cora was hit with a beer can and NESN reporter Guerin Austin said she was hit with a beer can while riding on one of the duck boats.
Patrick Connolly, 19, was arrested after the parade by Boston police for hitting someone with a beer can during the parade.
Officers arrested the Sandwich-native after they say they saw him throw an unopened beer can and hit a person on one of the duck boats.
Connolly was charged with assault and battery by means of a dangerous weapon and disorderly conduct.
Five others were arrested on charges ranging from underage drinking to drinking into public, to possession of narcotics.
The Associated Press contributed to this report.