One thing I wanted to point out is in your code you were jumping between late and early binding. I don't know if this was intentional or not, but ideally, you would only want to choose one. In my solution, I am assuming you want early binding.
Now the other thing I would recommend you do is to make sure you declare all of our variables so that way you can write your code a little more concisely and it's easier to know which object we are working with.
The reason you are having the problem could be a couple of different issues but one of them is possibly related to the clipboard. The reason I suspect this is that you're saying the error is sporadic, this usually is an indication of the clipboard error. Lucky for us there are a couple of solutions we can implement. My go-to solution is to pause the Excel application for one or two seconds to ensure the information makes it to the clipboard. This solution usually fixes 95% of the errors related to the clipboard.
With that said, it won't work 100% of the time. As strange as this may sound we can still have situations where the information disappears from the clipboard.
Also if you're new to Excel VBA & PowerPoint VBA working in tandem I have some YouTube videos that go over this topic. Feel free to check them out if you think you will want to do more complicated scripts.
https://www.youtube.com/playlist?list=PLcFcktZ0wnNlFcSydYb8bI1AclQ4I38VN
Try out this code and let me know what you get:
Sub Test()
'Declare Variables
Dim PPTApp As PowerPoint.Application
Dim PPTPres As PowerPoint.Presentation
Dim PPTShape As PowerPoint.Shape
'Create a new instance of PowerPoint
Set PPTApp = New PowerPoint.Application
PPTApp.Visible = True
'File Path
DestinationPPT = "C:\Users\Saeed\Desktop\edit vba\test.pptx"
'Open the File
Set PPTPres = PPTApp.Presentations.Open(DestinationPPT)
'Copy Range "A2" on the sheet.
Sheets("Slide3").Activate
Sheets("Slide3").Range("A2").Copy
'Pause the Excel Applicaiton for one second. This is for stability issues that may arise.
Application.Wait Now() + #12:00:01 AM#
'Paste the Range on the Slide
PPTPres.Slides(3).Shapes.Paste
Set PPTShape = PPTPres.Slides(3).Shapes(PPTPres.Slides(3).Shapes.Count)
PPTShape.Select
'Set Dimensions of Shape
With PPTShape
.Left = 17
.Top = 90
End With
'Save & Close the file
PPTPres.SaveAs "C:\Users\Saeed\Desktop\edit vba\" & Filename, ppSaveAsPDF
PPTPres.Close
PPTApp.Quit
'Release Objects From Memory
Set PPTApp = Nothing
Set PPTPres = Nothing
Set PPTShape = Nothing
End Sub