I'd suggest you look at your Lightroom Import options. It's very possible or likely that Lightroom was set to move the files into a specific location: a specific directory and possibly a subdirectory.
To check this out, you can do a fresh import: copy some pics into the location where you had copied the ones in question using your system file browser, as if you were doing a fresh shoot. Then, open the Lightroom Import dialog, then stop and carefully look over all your Import options, including the Import "action" selected in the list at the top of the Import dialog, and the "Destination"/"main" folder (it shows up in the top right corner as well as the "selected" folder in the Folder list down at the bottom of the right panels) and look at all of the options in the various panels on the right side, which should show specifics of how LR is set to handle the files as they are imported.
At least one of these options is likely not what you had suspected, but it should give you a "clue" as to where your files landed. You can verify this, but then I'd suggest you settle a workflow procedure so you don't have to mess with those options every time you want to do an import.
My workflow follows the KISS ("Keep It Simple, Stupid!") approach: I plug in the card from a shoot, and Lightroom typically opens the Import dialog (it's set to do that in my Preferences) and, by default, the LR action is to "Copy" the files from the card. In my file naming options I have a "template" set up (via the Edit option in the drop-down list) to name the files with a "custom text" with the date and shoot description, followed by a "xxx" three-digit sequence#.
After I type in the "base" text (date and description) then I Ctl-a (select the text/name) and Ctl-c copy it. I then go down to the panel designating the folder/destination and I make sure the "Subfolder" option is selected. I click on the Subfolder Name text box and Ctl-v Paste the base name into that text box.
That's it, two Simple steps, and I'll typically leave all the files/previews "checked" to import them all, so I just click Import, and it's a done deal, and the subfolder and images all show up in the Library module/Folders panel. Note that the files have been re-named from the names the camera gave to them.
As to the card, once the Import is done and the images show no problems, I'll delete the originals from the card using the camera Format function.
If you've gone over this and still can't nail the problem, well, let us know!