Sounds like you have some chart objects with zero width and or height.
This occurs when deleting rows/columns over which a chart is positioned. Rather than deleting the chart along with the row/columns the chart object is resized.
You could use this code to tell you how many chartobjects are actual contained on each sheet and their dimensions. Any with a zero width and or height will not be visible.
Sub XX()
Dim ws As Worksheet
Dim co As ChartObject
For Each ws In ActiveWorkbook.Worksheets
' Go through each worksheet in the workbook
Debug.Print ws.Name, "has "; ws.ChartObjects.Count, "chart objects"
For Each co In ws.ChartObjects
Debug.Print , co.Name, co.Width, co.Height
Next
Next ws
End Sub
If you then go to the sheet that contains more charts than expected you can use this command in the immediate window to select all the objects.
activesheet.chartobjects.select
If you then hold the CTRL key and select valid charts this will de-select them and you can simple delete the remaining selected charts.