They can be, especially in complex or lengthy novels. Authors have a lot to juggle, and it's not always easy to make everything seamless. Also, different readers might perceive plot inconsistencies differently.
One possible plot hole could be the time jumps that seem a bit inconsistent in terms of how the events are connected. For example, the sequence of the briefcase's journey and who has it at different times can be a bit muddled.
Since I don't know the exact 'holes story', I can only guess. Maybe the main plot is about a character who is on a quest to fill holes that are causing problems in their world. For example, holes that are swallowing up important things like crops or buildings.
Maybe the story is about a cave with 10 holes. Each hole leads to a different level of hellish nightmare. A group of explorers enter the cave out of curiosity. As they peer into each hole, they see visions of their worst fears - for some it's losing their loved ones, for others it's facing their own mortality. And as they move from hole to hole, they start to lose their sanity.
Take 'Cinderella'. The glass slipper is a major plot point. But think about it, how could a glass slipper fit only Cinderella's foot so perfectly in the whole kingdom? It's a bit far - fetched. Also, when the clock strikes twelve, all of her things turn back, but the glass slipper remains. It's not very consistent in the rules of the magic in the story.
Plan your story thoroughly before you start writing. Make sure all the elements fit together logically. Also, have beta readers review it to catch any potential holes.
One possible plot could be that Laufey, Loki's biological father, decides to use Loki against Thor. He might abuse Loki in some way, either physically or emotionally, to make Loki do his bidding, which could involve causing trouble for Thor. Loki, being in a difficult position, has to deal with his complex feelings for Thor while also trying to escape Laufey's control.
One possible plot could be that Izuku suddenly finds himself with Loki's powers and memories. He has to deal with the newfound ability to deceive and manipulate, which goes against his usual honest nature. He might use these powers to outwit villains in a different way than he usually does in his own story.
In the fanfiction, once Loki bows, it could set off a chain of events. Percy might gain a certain status or power boost because of Loki's submission. This could make him a target for other villains or jealous characters. Meanwhile, Loki might be seen as a traitor by some of his own kind. The plot could then revolve around Percy and Loki trying to deal with these new situations, with Percy having to protect Loki from those who want to harm him for his actions, and Loki having to prove his new - found loyalty to Percy.