There might be a powerful dark wizard who has infiltrated Azkaban and is using it as a base for his evil plans. He sees Harry and Daphne as threats to his plans and tries to stop them at every turn, whether it's by setting the Dementors on them or using other dark magic against them.
The Dementors could be the main antagonists. They are always a threat in Azkaban, sucking out the souls and happiness of the prisoners. They would be constantly trying to get at Harry and Daphne.
It could be some corrupt prison guards. They might be in league with dark wizards or have their own dark motives. They could make life difficult for Harry and Daphne, preventing them from finding a way to prove their innocence or escape.
It could be the corrupt prison guards or wardens. They might be in league with dark forces outside Azkaban. They oppose Harry and Ginny because the couple is getting too close to uncovering their illegal activities within the prison, like smuggling dark artifacts or collaborating with Death Eaters.
The Malfoy family could be antagonists. They might see Harry as an enemy still and not want Daphne, a pure - blood, to marry a half - blood like Harry. They could try to create problems between the two, spreading rumors or trying to sabotage their relationship.
In the 'Harry and Daphne baby fanfiction', it could be a new dark wizard who rises to power. This wizard might believe that the baby has some sort of power that could stop him from achieving his goals. So, he makes it his mission to eliminate the baby. Also, there could be some magical creatures that are being controlled by a dark force and are sent to attack Harry, Daphne and their baby because they sense the baby's potential power.
Some of the pure - blood supremacist families who still hold grudges against Harry could be antagonists. They might not approve of Daphne getting involved with Harry, seeing him as a threat to their traditional values. For example, some of Daphne's extended family members who are still stuck in the old ways could try to break them up.
In the fanfiction, it could be that Daphne has some unique magical ability that she uses to protect Harry in Azkaban. They might encounter other inmates who are actually innocent too and together they start a mini - revolution against the unjust system of Azkaban. Harry, with his experience of facing Voldemort, might lead the way in finding a way out of the prison.
The Dementors first and foremost. They don't really care about justice or innocence, and their actions are a form of torture. Then, there could be a new dark wizard or group that has emerged and wants to use Harry's situation to their advantage. They might have bribed the Azkaban staff or found a way to get in and torture Harry for their own purposes, like getting information about the Order of the Phoenix or just to create chaos in the wizarding world.
One likely antagonist could be Draco Malfoy. He's from Daphne's social circle and might not approve of her being with Harry. He could try to expose their relationship out of jealousy or because of his pure - blood supremacist views.
Dark wizards or witches who are on a power - hungry spree could be the antagonists. They might see Daphne as an easy target or a way to get to Harry Potter himself. So they kidnap her to lure Harry into a trap.
Obviously, Harry Potter is the central character. He's the one who is wrongly imprisoned in Azkaban.
Perhaps a new dark wizard or witch who has infiltrated the Ministry of Magic and made sure Harry was sent to Azkaban. This antagonist could be working towards a bigger plan to take over the wizarding world and sees Harry as a major threat even when he's locked up.