It's a good question, the whole "Biosphere" project which you can go visit in Arizona which sought to do something like this. It isn't underground, there really

It's a good question, the whole "Biosphere" project which you can go visit in Arizona which sought to do something like this. It isn't underground, there really isn't much advantage, and there is a whole lot of expense, in building under ground. So the partial answer is that people are doing this research. Complex interactive systems like this however are very hard to design all at once. One strategy might be to solve individual problems like having a habitat that provides all of its own oxygen and CO2 processing. Then once that is understood have one that can recycle 100% of bio-waste. Then add a long term power supply, then figure out how to make that supply a renewable one. It is a very complex process and each step will reveal new interconnections that need to be dealt with.