Four-time champions Ghana booked their place in Sunday's final with a 3-0 victory in Malabo on Thursday.
The mood within the stadium changed shortly before half-time, though, as certain sections of the crowd began to throw missiles after Ghana went 2-0 ahead.
Police were required to shelter Ghana's players as they left the field at the interval, and the trouble led to a 30-minute stoppage during the second half.
Both teams remained on the field as confusion reigned during the interruption, brought about when Ghana supporters gathered behind one of the goals to avoid being hit by missiles.
Tutu Alicante, the executive director for EG Justice, which works to promote human rights and the rule of law in Equatorial Guinea, is surprised that a similar incident did not occur before Thursday's match, and believes it was a mistake for the Confederation of African Football (CAF) to host the tournament in the nation.
"As anyone would agree, it was quite embarrassing to a nation that did not deserve the honour of hosting this tournament in the first place," he told Perform.
"The Africa Cup of Nations is supposed to be about what is good about sports, about what is good about Africa. Taking this tournament to Equatorial Guinea in the first place was a decision heading in the wrong direction.
"I was quite surprised it took so long for something like this to manifest. I expected something like this to happen."
Alicante believes the actions of those throwing missiles were not only a reaction to the scoreline, but also part of a wider social problem in the country.
"It's a combination of both things," he added. "When you live in a dictatorship and you don't have any avenues to express how you feel, to express what you think, to express anything, then things like this are likely to happen.
"You drink a couple of beers, your team is losing and you vent your frustration. It's not just frustration at the game, it's frustration from decades of living in an oppressed dictatorship.
"It's also symptomatic of what happens when you live in a place where everything seems to go in favour of the leaders all the time. We are used to our presidents winning elections by 99 per cent of the vote. We're used to seeing our team win whether by corruption or stealing penalties."
With Equatorial Guinea set to face the Democratic Republic of Congo in a third-place play-off fixture on Saturday, Alicante expects more trouble if security is not improved.
"I fully anticipate something happening in the third-placed match if it takes place," he said. "For the third-placed game I hope after what happened there they have plenty of security.
"I think you have to beef up security. [But we also ] have to look at this long term. To avoid similar embarrassing incidents, not just for Equatorial Guinea but for Africa, you have to be a bit more responsible for who gets to host this tournament.
"CAF should be a bit more responsible for how it hosts these type of tournaments. Otherwise you'll get these kind of incidents when you take these tournaments to a dictatorship."
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