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.
One idea could be exploring what would happen if Spider - Man had to team up with a villain to stop a greater threat. For example, partnering with Doctor Octopus to take on an alien invasion.
One key plot point is A - Day's disaster which splits the Avengers. Another is Kamala Khan's journey to reunite them. And the threat of AIM is also crucial.
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.