You appear to be mixing early binding and late binding for powerpoint in the same sub. Why? Usually, only one approach is chosen.

I skipped the dim parts and some unimportant ones.
From the perspective of someone taking the time to help you, they are not all that unimportant, since it means a lot of typing and/or guessing about that missing information if the problem is to be replicated.

My guess is that the problem is coming because you are trying to paste to the window instead of to the slide. Here's a potential alternative. 
 Sub Test()

    Set PowerPointApp = CreateObject("PowerPoint.Application")
    PowerPointApp.Visible = True
    DestinationPPT = "C:\Users\Saeed\Desktop\edit vba\test.pptx"
    Set ppPres = PowerPointApp.Presentations.Open(DestinationPPT)
    Sheets("Slide3").Range("A2").Copy
    With ppPres.Slides(3)
        .Shapes.Paste
        Set shp = .Shapes(.Shapes.Count)
        shp.Left = 17
        shp.Top = 90
    End With
    ppPres.SaveAs "C:\Users\Saeed\Desktop\edit vba" & Filename, ppSaveAsPDF
    ppPres.Close
    PowerPointApp.Quit
    Set ppt = Nothing