Controversies
- Format
South Korea completed the first two rounds undefeated (6-0) but was still forced to play Japan, a team it had already beaten twice, in the semifinal round. South Korea lost the match and subsequently was placed 3rd, despite the fact that South Korea's final standings were 6-1, with the most wins. Other international sporting competitions, such as the FIFA World Cup, are formatted so as to make it impossible that teams play each other three times. They can only face twice at most - in round robin group play and then again for the championship or 3rd-place match. In addition, the regional grouping of teams was called into question, for the groups were perceived to be unevenly distributed, and the four-team pool system and subsequent three-way tiebreakers were widely seen as awkward.
- Umpires
Tournament organizers were unable to reach an agreement with the MLB umpires' union and so the Classic was overseen by umpires from the minor leagues. American umpire Bob Davidson made controversial calls at critical moments in two different games that benefited the American team.
- Chinese Taipei
The Chinese Taipei team was originally listed as "Taiwan" and bearing the ROC national flag, but following pressure from the People's Republic of China the listing was later changed to Chinese Taipei with the Chinese Taipei Olympic flag.
- Drug Testing
The World Anti-Doping Agency criticized IBAF's drug testing program and threatened to withdraw sanction of the event. South Korean pitcher Myung-Hwan Park tested positive for a banned substance during the event, and he was subsequently kicked out of the WBC.. Venezuelan pitcher Freddy García tested positive for marijuana.
- Team Cuba
In an effort to enforce the United States government's embargo on Cuba, the Cuban team was initially denied a license to play in the United States. Puerto Rico threatened to pull out as hosts, IBAF said they would rescind its sanctioning of the tournament, and the IOC suggested that such a development would influence the ability of American cities to successfully bid to host future Olympic Games. As a result, financing was restructured and the U.S. government withdrew their opposition.
- Player participation
A number of Major League baseball players chose not to participate, some backing out at the last minute. Without players such as Barry Bonds, Vladimir Guerrero (who pulled out because 3 cousins died in a car accident right before World Baseball Classic), Manny Ramírez, Hideki Matsui, and José Vidro, some questioned whether the event would be credible. Cuba barred players such as Orlando Hernández, his half-brother Liván Hernández, and José Contreras, from its team, Cubans who had previously defected. Additionally, Italy utilized a roster of players made up almost entirely of second-generation Italian Americans such as Mike Piazza.
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