See what I did there.
Designing for 3D printing can involve a lot of Boolean operations where you combine or subtract parts together. If you have done this before you know it's a pain and often doesn't work well. Cinema 4D has great boole functions but I have run into a lot of problems combining all of these extruded parts.
Ideally, you want to design and combine all the parts as normal, single shell, primitive or box modeled parts. But since you have to extrude the parts at some point in order to print, sometimes it's necessary to extrude them for thickness first and then combine them. This can cause a ton of problems
Here's a walk through of a typical situation I've been dealing with and how to make it work.
UPDATE: In the video I mention NOT optimizing the parts in Cinema. After doing this for a while I have found it varies. Sometimes optimizing screws up things in MeshLab and netfabbb and sometimes it makes things work. Go figure. Depending on what part I'm working on, I may or may not optimize.
UPDATE 2: After further investigation this appears to be due to the point optimization tolerance of points and what scale you are working at. For the Octopod I was modeling at millimeter scale and you can only set the point optimization tolerance so small. This would cause points to merge that I didn't want to merge and cause weird geometry. In hindsight, it would have been better to model on a larger scale, like centimeters, then scale down everything for printing.