I'm running into this problem after doing myStore.removeAll() followed by myStore.add(record). When the grid's view calls updateIndexes(), the previous nodes whose records have been removed are still present. Calling myGrid.view.refresh() is a workaround. westy's override works as well.
This happens when there is a duplicate id in the the store. Two records with the same id causes an error like records[i] is undefined in updateIndexes. I fixed that, but now I am getting the problem in a Summary Grid
I had put a Grouping feature and a GroupingSummary feature on the same view. Then you get this error too. I fixed that!