When an document is open, corresponding file kept open. This is normal.
But lock should be removed and file closed when document is closed. Currently it's not happening.

Prepare 1.xls: create new spreadsheet, save it as Microsoft Office 2003 XML (.xml). You can keep .xml extension or change to .xls for easier opening (because of registry association). Close the file. I'll refer it as 1.xls in following examples.

Case 1:
1. Open 1.xls with LibreOffice.
2. Close document (Ctrl+W), but don't close LibreOffice.
3. Try to do something with the file (outside of LO), you'll fail. Check opened file descriptiors for LO (handles.exe or procexp.exe), you'll see that LO, despite file isn't open anymore, keeps it opened on system level.

Case 2:
1. Open 1.xls with LibreOffice.
2. Save it as 2.xml (or anything else)
3. Check as before. You'll see that 1.xls kept open / locked.
4. Close document (Ctrl+W), but don't close LibreOffice. 1.xls sill kept open, though 2.xml is properly closed.

Note that .lock files created and removed appropriately, despite file itself kept open.