There are manifests missing - at least from the on-line we sites. We had complete information for the arrival of my husband's grandfather in December 1899 - name of boat, date, etc. We even have correspondence that he wrote from the boat. We were unable to find anything on line. A few years ago we personally went to the Family History Library in Salt Lake City. After an approximately two hour search, my husband found the manifest in the library - the entire page of Hamburg arrivals was never put on line. We have sent it to Ancestry since then, but I don't think it was ever entered.
We still haven't found the arrival record for my husband's grandmother and father in 1900.
I'm sure that if we are missing records, many other people are missing records as well.
Avivah R. Z. Pinski , near Philadelphia, USA