Three people died in a crush in Conakry ahead of a World Cup qualifier on Sunday and another match in Monrovia was repeatedly stopped as police battled to control rioting spectators.
The three deaths occurred as fans sought to buy tickets for the African zone Group Five match between Guinea and Morocco, which ended in a 1-1 draw.
Eyewitnesses said the three who died had been trampled in a crush as a crowd of 35,00 sought to gain entry to the derelict September 22 stadium in the Guinean capital.
In Monrovia, Ivorian referee Aboubacar Sharaf twice stopped the Group One match between Liberia and Senegal after fans pelted objects on to the pitch as the home side conceded two second-half goals in a 3-0 defeat.
There was a brief stoppage after Senegal's second goal scored by Henri Camara and when the Celtic striker scored their third 15 minutes from time spectators again rioted forcing a delay of almost 30 minutes.
Senegal's away win kept them top of the standings, although only on goal difference from Togo and Zambia.
Emmanuel Sheyi Adebayor scored early to ensure Togo beat Mali 1-0 in Lome, while Collins Mbesuma grabbed a hat-trick in Zambia's 3-2 away triumph over Congo in Brazzaville.
Mbesuma put Zambia three goals ahead before Congo staged a late fight back to reduce the deficit with a double strike from Armel Mamouna-Ossila.
Ivory Coast took a two-point lead in Group Three after Aruna Dindane got the only goal in their 1-0
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The Ivorians, emerging as the form team of African football, benefited from setbacks for their closest rivals Cameroon and Egypt over the weekend.
Egypt lost 2-1 in Libya on Friday, while Cameroon scrambled a last-gasp equaliser for a 1-1 draw with Sudan on Saturday.
Benni McCarthy's penalty midway through the second half gave South Africa a 1-0 away win over Uganda in Kampala on Sunday to put them top of Group Two.
It was the first away win for any team in the group and South Africa also benefited from a 0-0 draw between previous leaders Ghana and the Democratic Republic of Congo in Kumasi.
The result is a setback for Ghana who were playing their first match under caretaker manager Sam Arday following the departure of Portuguese coach Mariano Barreto last month.
Angola striker Flavio's goal put his country top of Group Four after a 1-0 home triumph over Zimbabwe in Luanda on Sunday. They are surprisingly a point above Nigeria who were held to a 1-1 draw in Gabon on Saturday.
The qualifying competition in Africa has reached the halfway stage and will resume again in March with the exception of Kenya who have two catch-up games to play in Group Five.