Enyimba of Aba, Akwa United and Shooting Stars Sports Club of Ibadan are the four Nigeria Professional Football League sides that crashed out of the Federations in the round of 32.
Four-time winners Enyimba were beaten by Plateau United 3-2 on penalties after regulation time ended 2-2 at the Samuel Ogbemudia stadium on Wednesday.
Plateau came from two goals down to force the game into shootouts.
At the Dan Anyiam Stadium in Owerri, Nigerian National League side Warri Wolves defeated Shooting Stars 4-3 on penalties to advance to the round of 16 after both teams failed to score in regulation time.
At the Abubakar Tafawa Balewa Stadium in Bauchi, Nassarawa United who were recently relegated from the NPFL put behind them their poor performance this season to edge DMD FC 3-2 in a pulsating encounter.
In Calabar, League leaders Bendel Insurance kept their hope of winning a domestic double alive after a narrow 1-0 win over Ahudiya FC.
Sarki’s second-half strike sealed a round-of-16 spot for the Benin Arsenal.
At the Lokoja center, Sunshine Stars of Akure beat Standard FC 2-0 courtesy of a brace from Micheal Olalusi.
Olalusi scored in the 13th and 77th minute of the encounter.
Akwa United were also dumped out of the competition after they lost 9-8 on penalties after full-time scores were level at 1-1.
Enough Rangers also got a narrow 1-0 win over Kano Pillars in Abuja to seal a place in the round of 16 while Kwara United beat Ikorodu City 3-1. Heartland FC were 2-1 winners over Essien Ayi just as Insurance Feeders beat Osun United 2-1.