The most common way a protagonist loses definition across a long manuscript is ensemble pressure. You introduce supporting characters. Some of them turn out to be more interesting than you expected. You start giving them more space. Subplots develop. The narrative sprawls outwards in ways that feel generative and alive.
And meanwhile, your protagonist is being slowly crowded out of their own story.
It's not that the supporting characters are too vivid. Vivid supporting characters are good. The problem is when scenes start to exist for the ensemble rather than for the protagonist's journey. When your protagonist is present but reactive, or even not present at all. When they're the person to whom other characters explain things, rather than the person whose choices are driving the story.
Subplot sprawl compounds this. A subplot that doesn't eventually bear on the protagonist's central want or wound can be entertaining in isolation, but it forces the reader to spend attention somewhere other than the protagonist. Do that enough times and the reader loses the thread of who they're supposed to be following.
A great example of this is my current read, Arm of the Sphinx, the second book in Josiah Bancroft's Books of Babel series. And I have to say, I'm struggling with it.
The first book, Senlin Ascends, is told in tight third person - no slip from the perspective of the main character, Thomas Senlin. I loved the book, found Senlin an engaging protagonist, and couldn't wait to start the second book. But I soon ran into what felt like mud.
In Arm of the Sphinx, Bancroft appears to have given in to pressure from, or love for, his supporting cast. In this book, we now have entire sections, even chapters, that drift about between the other characters with Senlin on his journey. I enjoyed them all in the first book as supporting characters. But now they're all vying for my attention and it just feels messy. Worse, I'm forgetting what Senlin did because a whole chapter has passed, seemingly just to get another character to him, and explain what has happened in the wider story, none of which was really necessary.
The question you need to ask of every scene that doesn't centre on your protagonist (and Bancroft arguably didn't): does this scene or chapter change something the protagonist will have to reckon with? If the answer is no, it might be working against you.