Complex sentence: Controversy arose during the 2006 World Cup Qualifiers, when the team's supporters caused problems because of lack of qualification; however, in 2009, the team qualified for the 2010 FIFA World Cup, the second World Cup appearance in their history.
Split into simpler sentences: Controversy arose during the 2006 World Cup Qualifiers, when the team's supporters caused problems because of the team's failure to qualify. In 2009, the team qualified for the 2010 FIFA World Cup, the second World Cup appearance in their history.