Hey there, I've looked into the imagery and I believe that these are not inner courtyards, but a break in the roof where one can find utilities such as air conditioning units. 

As someone that also made a similar mistake when starting out, I will tell you that you did this wrong. If you want to create a courtyard, then use the line tool (the second option) and make a square inside the building. Afterwards, merge the square and the building, and now you will have an empty space inside the building. In the manner that you did this here, there is now a building inside of the university buildings, which is erroneous. 

If you wish to add different elevations to a building in different sections, then use the building:part component. There are multiple examples around the city that I've personally created for you to guide yourself.