However, he said this was partly because Italians enjoy controversies and suggested that, in principle, the video replay system (VAR) was a good idea.
Juventus, second in the table, won 1-0 at Cagliari on Saturday but the Sardinians were angry over two decisions.
They claimed that the move leading up to Federico Bernardeschi's 74th minute goal should have been stopped after Leonardo Pavoletti was elbowed by Medhi Benatia, but the referee allowed the goal to stand without consulting the VAR.
Shortly afterwards, Cagliari demanded a penalty for handball by Bernardeschi when the ball hit his outstretched arm.
The referee turned down their appeals without watching the video replay himself, although Italian media said he was given advice by the video assistant via his earpiece.
"The VAR was introduced to reduce controversies and instead they have increased, possibly because we Italians like to stoke them," said Allegri.
"We look for controversies instead of analysing the match -- Cagliari played a really good game and didn't deserve to lose.
"This is obviously the first year VAR has been put into use and next season we will have more clarity."
"The referees are doing really well and will learn how to use it for the most eye-catching incidents. For example, it's fundamental in judging offsides."
He added: "In every match, there a difficult decisions, sometimes they go in your favour and sometimes against. You need to be able to accept them."
Serie A is one of several competitions around the world where the VAR system is being used on a trial basis.
Soccer's law-making body IFAB is due to decide in March whether to ratify its use on a permanent basis and, depending on the decision, FIFA are hoping to use it at this year's World Cup in Russia.
(Writing by Brian Homewood in Bern; Editing by Amlan Chakraborty)
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