"BUG-000101315: In some cases, the Minimum Bounding Geometry tool with option Rectangle By Area and the List option does not include all features of the categories within their respective bounding boxes.
The report will be evaluated by the product teams for addressing in a future version or patch. In the meantime, a work-around is to run the Points To Line tool using the point layer's category field for the Line Field of the tool. The Sort field in the tool is not necessary in this case, nor is Closing the line. Use the resulting line feature class as input to the MBG tool with the Rectangle By Area or Rectangle By Width option. A rectangle enclosing each group is created, although it is wider than necessary."
I was using this tool in an arcpy script. Another solution was to update the xy tolerance and resolution, but it must be set back afterwards lest it break another tool in your script.