Hello @kokebdese
Sorry for the late reply.
Previously, we where looking at the Betti numbers, which are only related to the geometry. The persistence diagram however make sense for a scalar field defined on a domain. It will track how the connected component of the scalar fields evolve as we sweep the scalar values. The full explanation would be available here.
Also, be careful, if visually this diagram seems to have 3 branches + the diagonal, it has 13 cells in the information tab on my side (it may be a bit different for you depending on the elevation you used). If you have watched the video, this is because the elevation may have induced very small features (noise).
In my case, by removing the pair with a very small persistence using a threshold, I could get the good result:
Ten pairs + the diagonal that correspond to the min-max feature.
This is definitely not the way to count topological holes.
You may want to try the persistence generator if you want to extract those holes, an example can be found here.