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@ahmetsarikaya,
This behavior is by design and datapoints are sorted in case of scatter and bubble charts. In your case, you can have a key that stores the index of the datapoint being passed and use that key to delete the particular datapoint as shown in this JSFiddle.
If you are still facing issue, kindly create JSFiddle reproducing the issue so that we can look into code, understand the scenario better and help you out.
— Shashi Ranjan Team CanvasJS