On the contrary. It took square mile after square mile of facilities, constructed at the cost of billions, in several states.
No, you're thinking of uranium enrichment, which is a very large-scale and difficult engineering endeavor. Even then, the "square mile after square mile of facilities" was mostly required because we were trying a number of different approaches to the problem. Plutonium separation, by contrast, is an easy chemical process. All the plutonium needed by the Manhattan Project was produced in this one building at Hanford:
You can determine the scale by comparing it to the cars in the parking lota few hundred yards long, so bigger than one football stadium but by no means impossible to hide underground. It is completely believable that al-Tuwaitha could have a plutonium refinery in its basement.