school project, stuck , layers mix each other

Im trying to combine three layers into a pdf for a school illustrator assignment, but whenever i do it the layers keep getting mixed up, and one specific part of all layers mixes with the others, a square shape at the bottom of the page, that i guess confuses the program into combining the three layers in all the pdf. How do i fix that? I did the outline for all the things also. 

please help i dont know how to fix it