Apologies for the slow response; I saw this follow-up question just now!
You are seeing this error because there are a total of 11 invalid footprint geometries (in this case, multi polygons that are not nested) in the provided GeoJSON. Anytime FootprintHandler hits one of these geometries, it throws a fatal error. Please see attached images for five randomly selected samples from these invalid footprint geometries.
I pushed an update to FootprintHandler so that it successfully bypasses such footprint issues. Please let me know if you have any problems after updating your BRAILS setup to the latest.
On a side note, I see that this GeoJSON was generated using OSM. When I look at the current footprints for the 11 problematic locations in the provided GeoJSON, I currently see valid footprints. I wonder if this issue has to do with the way the footprints were extracted from OSM. If you can share more information on the specific process used to obtain these footprints, I might be able provide suggestions that may eliminate this type of footprint extraction issues.