basically the lid is too,large - if you load both into simplify3d you can clearly see the lis is larger than the box.
So a simple fix is just resize the lid.
that can be done in a slicer, or in the cad program.
box and lid.JPG


Also the lip at the end is higher and larger diameter than the piping along the sides . Given that all the indents are the same size and aligned.
That is also an issue :-)

It would be a 1 minute fix in openscad - not a clue in fusion 360.