yes you have errors in your data.
#N/A

here is a lazy workaround but the obvious solution is to not have errors.
also adjusted how the filter works to work with your data

Sub HighlightUniqueDuplicatesGC()
Dim sh As Worksheet, c As Range, clr As Variant, lr As Long
Set sh = ActiveSheet
lr = sh.Cells(Rows.Count, 6).End(xlUp).Row
clr = Array(3, 4, 6, 7, 8, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 53, 54)
With sh
.Range("F1:F" & lr).AdvancedFilter xlFilterCopy, , .Range("EE" & lr + 2), True
x = LBound(clr)
For Each c In .Range("EE" & lr + 4).CurrentRegion
On Error Resume Next
If c.Value = "#N/A" Then
c.Value = "N/A"
End If
On Error GoTo 0
.UsedRange.AutoFilter 6, c.Value
If Application.CountIf(.Range("F:F"), c.Value) > 1 Then
.Range("F2", .Cells(Rows.Count, 6).End(xlUp)).SpecialCells(xlCellTypeVisible).EntireRow.Interior.ColorIndex = clr(x)
End If
.AutoFilterMode = False
x = x + 1
If x > UBound(clr) Then x = LBound(clr)
Next
.Range("EE" & lr + 2).CurrentRegion.Delete
End With
End Sub