It almost certainly has nothing to do with Operation Paperclip. While the Naval Amphibious Base Coronado was established in 1944, the buildings in question weren’t built until 1967-69. By then Operation Paperclip was well over.

The official explanation is that it was an oversight. The six buildings were designed separately. In fact the original design was for facilities and recreational building, with a single L-shaped barracks to be attached. When they decided to expand the design, the instructions were to simply copy the initial barracks design. It wasn’t until construction started that they realized that the four L-shaped barracks together formed a Swastika. A version of this can be seen in this letter sent to The Power Hour, and in similar responses to other media outlets.

There’s been a lot of speculation since the shape was publicly discovered. But so far no one has documented a better answer than the one given by the Navy. No one has come forward with a site plan that shows all six buildings, or any other documentation to indicate that the Swastika design was intentional. If it was a conspiracy to secretly delight some unknown group of Nazis, there hasn’t been any proof yet discovered.