I assume you are using copy in Import.
I don't see any sub-folders in the screen shot posted.
The target location is defined during the import: How to transfer photos from a camera or card reader to Photoshop Lightroom
Check your settings and the preview in import dialog that shows you exactly where the images will go.
When you import from a card Lightroom has to copy the images to your drive before it actually imports them. The right side of the import dialog screen (assuming you are using the expanded view) shows you where the images are being copied. There are options to organize by date, or to put in a sub folder with a specific name. Examine the right side of the import panel carefully before starting the import. You should be able to figure out what is happening and how to fix it.