Now about why it's duplicated. In the "Projects" view all tasks marked as projects are listed recursively, therefore embedded projects will show up:
a) For the first time as a part of the parent project;
b) For the second time as an independent project.
To avoid confusion, in MLO-Windows bring up the "Filter" pane and click on "Config" in the "General" section. Remove a checkmark next to "Continue searching in branch after main filter match". In MLO-mobile open "Custom View Settings" for the "Projects" view and disable "Continue searching in branch". The smaller projects will be only shown once as parts of the main project.
Also, you may focus on the parent project (use "Zoom in") to work on the smaller projects.
Do not delete sub-projects in the "Projects" view since they are not duplicates. If you are not sure, feel free to check the whole structure in the Outline (the "All tasks" view).