Well two things could be at work here.
First, the plot could truly be at fault, non-cohesive, or missing some of the elements. Those elements are a central problem the main character tries to solve throughout the story (if there's no central problem, there's no story); complications that arise from efforts to solve the problem, that fail; a bleak moment, when it looks as if all efforts will fail; followed closely by the climax, in which the problem is faced head on; the resolution, either happy or sad, where the problem is solved or not.
Or noncohesive could mean there's too much "good stuff" that happens to the character between the bad stuff. Don't stop the story for a carousel ride. Keep the character at risk of losing everything all the time. My friend Carla Neggers says the way to plot is to put your character in a hole and every time they try to climb out, throw more dirt down on them. If you throw enough dirt, according to Carla, the Big Gloom (don't you just love all these technical terms) her term for the bleak moment, will arrive without looking contrived. This can be hard to do, because most of us love our characters and we enjoy writing the parts where things are going well. Readers, however, want to get on with the story.
Second, it might be the writer's inability to "tell" those elements in a simple, abbreviated, synopsis form, without embellishment or including unneeded detail. If she puts lots of stuff that isn't part of the plot into her synopsis, you have no direct plot line from beginning to end, but a wandering path. And the agent, looking at that wandering path, may well say "all over the place." Even though the story itself is a good, and well-written one. Writing synopses is an art form of its own, one that breaks all the "rules of good writing" and it would behoove us all to learn to do it well and briefly. My advice for that kind of writing is to the point: TELL ALL.
Boy meets girl and they fall in love, but their families have a longstanding hate relationship. (Central Problem)
Boy and girl secretly elope despite objections from both sides (complications that arise from the central problem), that keep them apart. They decide to run away together.
Girl fakes suicide in order to escape her family and go live with her husband.
Husband finds her, believes she is dead, kills himself. (climax)
Girl comes to, discovers her husband dead, and kills herself. (resolution, as the family war is no longer of consequence to either of them)
And, yes, you're right, the plot IS Romeo and Juliet.