Formula (VBA generated) fills the entire column of selected cell

Rodrigo_ Your data is in a table. In tables it is good practice (as in many other areas of a spreadsheet) to have the same formula in all rows (one that can be copied across), rather than ad-hoc formulas all over the place. That being said, your problem is being caused by a setting that enforces this: If you type a formula in an empty column of a table, Excel automatically copies that formula to all cells of that column. That can be turned off (though I do not recommend it!):

Private Sub Worksheet_BeforeDoubleClick(ByVal Target As Range, Cancel As Boolean)
    Dim r As Integer
    If Not Intersect(Target, Me.Range("F3:R65")) Is Nothing And IsEmpty(Target.Value) Then
        r = Target.Row
        Application.AutoCorrect.AutoFillFormulasInLists = False
        Target.Formula = "=IF($C" & r & ">$D" & r & ",$D" & r & "+1-$C" & r & ",$D" & r & "-$C" & r & ")"
        Application.AutoCorrect.AutoFillFormulasInLists = True
        Cancel = True
    End If
End Sub