Coaches and players have been angry about bizarre refereeing performances at several key matches at the tournament in South Africa but Hayatou believes that overall the standard has been good.
"Overall we are satisfied but we experienced some mistakes with the referees especially at the semi-final between Ghana and Burkina Faso, and there were other errors too...also at the Tunisia v Togo match," he told a media round-table meeting on Friday.
CAF took the unusual step on Thursday of announcing that Tunisian referee Slim Jdedi had been suspended following his handling of the game in which he awarded Ghana a soft penalty, denied Burkina Faso two far more obvious penalties and ruled out what appeared to be a legitimate Burkina Faso goal.
Burkina Faso won the match 3-2 on penalties after it had finished 1-1 following extra time.
Jdedi's most contentious decision came three minutes from the end of extra time when he showed Burkinabe winger Jonathan Pitroipa a second yellow card and sent him off for diving in the penalty area which means, pending appeal, that Pitroipa is ruled out of Sunday's final against Nigeria.
Television replays clearly showed that Pitroipa was fouled in the incident and that Jdedi had a clear view of the foul.
Other refereeing foibles included Ghana's goalkeeper receiving a yellow card instead of red for a handball outside his area in what was a blatant professional foul against Mali.
South African referee Daniel Bennett booked the wrong player, awarded two soft penalties and denied another obvious spot kick when Togo met Tunisia in Nelspruit.
Egyptian referee Gehad Grisha awarded a highly controversial penalty to Zambia in the last minute of their group match against Nigeria and subsequently was not given another game to officiate in the tournament.
After the match the Nigerian FA sent a strongly-worded protest to CAF, and Nigerian goalkeeper Vincent Enyeama described the call as "one of the worst decisions in the history of football".
Enyeama received no penalty or reprimand from CAF for his comments.
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