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In a statement, Malappuram FC said at least three 'key decisions' cost them their home match against Kannur Warriors on Wednesday.
A contentious offside call in the 65th minute denied the hosts an equaliser.
Two Brazilians scored in added time, the equaliser coming in 90+7, to make it 2-2 for Magic.
CK Vineeth-led Magic had lost their first two matches.
The South African's 76th minute strike made it 1-1 for Kochi.
The Kombans won 2-0 in their first game at home with goals coming in either half.
Basanta Singh scored the equaliser in the 76th minute after David Grande scored the opener for Kannur in the 11th minute.
Both the goals came in the first half of the contest at the Corporation Stadium in Kozhikode.
Magic had led the match until the 70th minute, but received a red card and lost thereafter.
Faslu Rahman and Pedro Manzi scored for Malappuram in a 2-0 win.
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