Booleans are notorious for leaving behind less than ideal geometry in your models. This is pretty much true for all applications, not just Cinema 4D. If you do have to use booleans in your modeling workflow, for what ever reason — you should learn how to create a chamfered or beveled edge on the boolean operation.

how to overcome one of the drawbacks of Boolean Modeling in Cinema 4D

Here, CyBear shows how you can overcome the drawbacks of using the boolean tools in Cinema 4D, by softening the hard edges for boolean intersections. This can be done without even making the polygon editable. This means that you can still have the benefits of the “live” boolean operation left behind.

Adding a chamfered edge to a boolean operation in C4D requires the use of “hidden” polygon selections. Thankfully, these are available in pretty much any of the spline generators, including boolean objects. Then it can just be a matter of using the standard bevel deformer to give yo the rounded edges you need in your model.

Keep in mind there are more ways to create holes in objects, rather than using booleans. A while back Shane Benson had a series of tutorials that covered subdivision modeling in Cinema 4D. He showed a few different methods for creating complete or partial holes on the surface of an object. Manual methods like this may take longer to produce, but they will give you a cleaner result in the end.