For a while now I've seen the issue where a tile package is created and uploaded to ArcGIS Online, but when published as a hosted tile layer you do not get 100% of the tiles for one or more scales. Republishing either from the Publish Tiles button on the layer's Settings page, or again from the uploaded tile package has not resolved the issue in my experience - I have to start from the beginning of the process; recreate the tile package and try again. Often a second try (with no changes made) will work. I've seen this when both uploading as part of the tile package creation, or when uploading from a PC after creation.
This does not happen every time, but it is often enough to be a nuisance - and can take a significant amount of time depending on the size of the layer. This has been with desktop versions 10.4 - 10.5, and on a few different machines. I haven't found any rhyme or reason yet...