merge object without intersecting faces for 3d printing


I’m new to Blender and tried to create some simple objects to print with my 3d printer.
I tried to merge objects using the boolean modifier, but it resulted in intersecting faces. Most of the time
these can be fixed by moving some vertices just a little bit, but there are too much of them to it all the time manually. Is there a better way to merge objects or did I miss something?

Before union:

After merging with the Cylinder faces are intersecting everywhere:

But intersecting faces even occur when I try to merge to spheres:

Thank you