If you rename a crate, or move it to a subcrate, while Serato DJ is still importing files to it (for example after dragging a folder to the crate list) then further files imported during the folder scan will not appear in the new crate.

Workaround:
When importing files by dragging folders into Serato DJ, ensure that the import process is complete before moving or renaming any crates. You can tell that Serato DJ has finished importing files by checking that the status bar at the bottom of the Serato DJ window no longer displays "Scanning Folder:" or "Reading Tags:".