Equatorial Guinea used an ineligible player (Thierry Fidjeu Tazemeta) in both legs of the AFCON 2015 first round against Mauritania.
Mauritania won the first leg 1-0 and lost the return leg 3-0.
Looking at article 36 of the AFCON regulations (2012 version):
36.11. A team which allows a non-qualified or a suspended player to take part in a direct knock-out match shall lose the match and shall be eliminated from the competition, even in the absence of protests.
36.12. A team which allows a non-qualified or a suspended player to take part in group matches shall lose the match by penalty (3 – 0), even in the absence of protests/reservations.
As far as I can tell, both matches should have been awarded. However, CAF only chose to kick out Equatorial Guinea and reinstate Mauritania.
The results still stand (see AFCON results on CAF's website).
Moving on to Seychelles. They withdrew after playing the first leg vs. Sierra Leone.
If, for any reason whatsoever, a team withdraws from the competition or does not report for a match, except in cases of force majeure accepted by the Organising Commission or refuses to play or leaves the ground before the regular end of the match without the authorisation of the referee, it shall be considered looser and shall be eliminated for good from the current competition. The same shall apply for the teams previously disqualified by decision of CAF.
The guilty team under the terms of articles 57 and 58 will be eliminated for good from the competition. This team will lose its matches by 3-0 unless the opponent has scored a more advantageous result at the moment when the match was interrupted, in this case this score will be maintained.
Again, the return leg should have been awarded 3-0 to Sierra Leone.
Because CAF did not official announce forfeit decisions for these cases, both Sierra Leone and Mauritania are ranked lower than they should be if these regulations were followed.
I wrote to CAF, Sierra Leone FA and Mauritania FA. No answer.