Thanks for the file! That really helps:
first, your top Faces that should be flat are not, which you can see in the Front and Side Orthographic Views:

Select them and then pres S, Z, 0.
Then there also some Double Vertices that are causing problems (especially with the Bevel Modifier).
Select everything (press A, in Edit Mode!) and then M > Merge by Distance.
I think that is all, but let us know if there are still issues left that I may have missed.