This is probably because the extra datasets do not have the same Feature Types as your workspace. When  you created the workspace, FME scanned the dataset(s) you selected to create a list of Feature Types; these Feature Types were added to the workspace; for example roads, rivers, railways. Now you are using datasets with different Feature Types taht FME doesn't know about. So, if you are translating files with fences, hedges, and ditches, they don't match the know Feature Types (roads, rivers, and railways) and FME will ignore them. You can see this in the log window - search for the line that includes the words 'Unexpected Input Remover' - this indicates how many feature have been filtered out with unknown Feature Types.I