Oxygen Not Included does that really well IMO. Almost every production process has inputs and outputs, and a lot of the outputs are waste that you need to figure out either how to utilize as input in another process, or to dispose of safely and in a scalable way so as to avoid negative repercussions. Waste isn't just in the form of products either. For example, one of the challenges that sneaks up on new players is that heat is also a type of waste, and if you don't take steps to manage it (for example, by insulating your power generators), it can wreck your colony.