Probably, the two table have a column with the same name, forcing Qlikview to link them. You can use the command unqalify * before the load commands. The unqualify command changes the name of the columns, concatenating the name of the table in front of the column names. This will result in columns with unique names in both tables.
You can also inspect the current (bad) relations using the Table Viewer (use Ctrl+T, it's a great tool) in QV Desktop. All connecting lines between the two tables should be eliminated.
If there aren't too many false relations created by QlikView, you can cut them by renaming the columns that cause these relations in only one of the two SQL statements. This is done by specifiying a new name immediatly after each offending column specification, like in
SQL SELECT "OriginalColumn1Name" "NewColumn1Name", "Column2", "Column3" ...