INADEQUATE WRITING SKILLS OR STORYTELLING/ STRUCTURE PROBLEMS.
In the case of the former, the writing itself does not display the energy, creativity, and polish necessary to convince an agent to go deeper. This is perhaps the number one cause of failure (and obvious on the first page). Usually, the writer is not aware--or at least, not sufficiently aware to enable productive change. Perhaps this is a first stab at fiction, she or he not realizing that tech or law or medical writing ill prepares one. Also, the writer does not know a good editor or reader, and therefore, has never received truly helpful crit. Or perhaps an ego obstacle is the issue. Also, we have the "birthed baby" phenomenon: the writer has produced a passage, a character, or scene they can't possibly do away with. It is sacred to them. So it remains, defacing the narrative like a major pothole, jolting agents and publishers alike each time they meet it.
In the case of the storytelling/structure issue, the writer may be very accomplished at connecting the word dots. The agent or publisher gives it a good read then backs off. Why? Well, the story goes nowhere. It is insufficiently interesting, quiet, or perhaps even confusing. Just recently a fine writer handed us a sample of his ms. His prose skill kept us turning, but finally, we bogged down on characters who spun endlessly in place, who never really took action or engaged in any reaction worth noting.