Sporting scored what proved to be the winning goal in Thursday's 2-1 triumph in first-half injury time.
But Reja felt too much time had been added on.
"The rules clearly state that the referee should blow the whistle once the injury time is over," Reja said. "Yet the referee went for 23 seconds more, and then even after they scored, he continued.
"I just don't understand the way he calculated time."
Sporting had a man sent off early in the second half but held on for victory.
"My players were gutted after the game and it's understandable as they did everything to try to bring home a result," Reja said.
"But we have to turn the page and focus on Sunday's game in Florence which will be a difficult one."
A win on Sunday would be a big boost in confidence for the Biancoceleste ahead of the Rome derby, which will take place after the international break.
Fiorentina, meanwhile, go into their encounter against Lazio on the back of a goalless draw at Napoli.
The result lifted the Viola to fifth place, two points clear of Lazio.
"I can only congratulate my players because it's not easy to come away with the Stadio San Paolo with a point," Fiorentina coach Sinisa Mihajlovic said.
Fiorentina's main strength has been their backline, having conceded only two goals in the four games so far.
Mihajlovic, whose side remain perfect at home this season, is still without injured striker Alberto Gilardino.
Jovetic will again lead Fiorentina's attack alongside Santiago Silva.