As per my discussion with @springmeyer in #284 there appears to be an issue with the support of GeometryCollections when creating tiles from geojson.
In some cases the features appear to be dropped across tile boundaries, though I have been unable to determine what the exact offending circumstances are. I isolated a cleaner test case from one of the culprit data sets, which you can get here.
I am using https://github.com/mapbox/mapbox-tile-copy v5.1.1 to generate the tiles but I tested with the latest release as well, and the issue persists.
Here is what the feature is supposed to look like (I flattened the geojson in this example using https://github.com/Turfjs/turf/tree/master/packages/turf-flatten):

And here is what it looks like without flattening the geojson:

I've created a working example here.
Please let me know if there is anything else I can provide to help isolate the problem.
Cheers.