Hive table and the Hive table is pointing at a location or directory which has several sub directories and each sub directories has files underneath it. When you query the hive table however, Hive is only reading the files at the top level folder and ignoring all the files under inside the sub directories.
There are two properties and need to make sure to set during Hive execution. If recursive directories/files are common in your environment and make sure to add the below properties to the hive-site.xml rather than setting this property at the application level.
SET hive.mapred.supports.subdirectories=TRUE;
SET mapred.input.dir.recursive=TRUE;