I have a site collection with root web and subwebs. The full crawl is indexing everything in the root web and subwebs. The incremental and continuous crawls only indexes the content in the root web, but never takes the content in the subwebs. None of the the items inside the subwebs are logged by the incremental crawler in the crawl log, not even errors.
I have however another site collection with a similar structure, in the same farm, but there, the full, incremental and continuous are working properly in webs and subwebs.
SharePoint patch level is December 2018.
I even tried CrawlLog.RecrawlDocument() but the crawler still seem to ignore the items added to the queue like that.