The Portuguese-speaking trio were excluded from practising with the rest of their team-mates due to disciplinary reasons
Havutcu replaced former coach Carlos Carvalhal in early April and following the 2-0 loss to city rivals Galatasaray at the weekend, the 41-year-old decided to take action.
The club announced on their official website that the trio had been excluded from squad training due to "a lack of discipline and issues with their personal lives."
They will continue to be excluded from squad training in the build up to this weekend's Super Lig Championship play-off fixture against Trabzonspor.
Meanwhile, Cenk Gonen is another step closer to returning from injury as he received treatment before undertaking some running exercises.