When you say the PurePath does not match the web request do you mean that you are missing some elements in this PurePath that are showing up in other paths? What technology are you monitoring? Do you have any screenshots to compare what you are seeing in the other PurePaths that this one is not displaying?
Is it a matter of your application A not having a high number of PurePaths like application B? I would suggest making sure that you are not drilling down through a problem analysis. Sometimes when I view a problem and then move to purepaths, the new views are filter based on the entities involved in the problem I just viewed. Simply look at the tab history and make sure there are no problems in the list.
Another thing would be to ensure you are drilling down to PurePaths at a similar point in the service flow. If you click on a service that is called at the end of the service flow you will have much fewer PurePaths than at the beginning.
Finally, each app is different. You said they have similar backend but there could still be large differences in the number of Purepaths depending on how the frontend calls those services.