I wonder whether what you're calling a plot hole might really be a character hole.
Go deeper into the character. Does your character think contradictory thoughts because you don't understand the character very well? If so, that's a character hole. Solve that by going deeper into the character. Find out more of the character's thoughts, especially the character's reactions to the people, places, and events of the story. You can find those thoughts by writing them. You don't have to keep them all in the manuscript.
Use contradictions to cause trouble. Contradictory thoughts can be awesome for fiction. They create dilemmas for the character. They create conflicts with other characters, who see the character as capricious, or hypocritical, or unfair. One way to handle contradictory thoughts is to feature them. Make the contradictions cause trouble for the character. At very least, have other characters comment on the contradictions.
Resolve the "contradictions." Another possibility is to demonstrate that the "contradictions" are not contradictions at all--find some way that the seemingly opposing thoughts are compatible. Again, the trick is not to eliminate the contradiction, but to feature it, this time by resolving it.
Force the character to do something contradictory. Another way to create a character hole is to plan the character's reactions around the plot. If you're pantsing, perhaps you're not doing that... but check. If you need the character to do something for plot purposes, instead of making the character do something out of character, change the situation to eliminate the other things that the character would rather do.
Motivate "unbelievable" actions. Another way to create a character hole is to leave a surprising action or reaction unmotivated. If the character does something that surprises you, you can cycle back to an earlier point in the manuscript and plant a little seed in the reader's mind.