He has allegedly concealed his back problem, and also went against a decision by the coaches and the team management to field first after winning the toss.
It was Sri Lanka Mirror that broke the news about the second issue.
Kapugedara led the team in the absence of Upul Tharanga, who is facing a two-match ban for a slow over rate in the second game.
Meanwhile, Kapugedara is unlikely to play in the fourth ODI at R. Premadasa Stadium today (31),
In his absence, Lasith Malinga will lead the team, reports say.