Perhaps there is a way to get what you want, but it will depend on the specifics of your situation. Please keep in mind that control systems (and therefore control charts) will typically collect data at regular intervals or over regular areas. Therefore JMP is expecting this as should any control charting system.
I assume you used the Control Chart Builder. From the red triangle popup menu, choose Show Excluded Region. The purpose of this command is that it will automatically adjust the Y-axis as if the excluded data did not exist. However, if you do NOT have a label for the x-axis, it will effectively remove that row from the display.
If you DO have a variable specified for the x-axis, the label will still appear for hidden and excluded data. That is by design because in a control chart, you are supposed to show all data, even out of control conditions. (although you often do remove from the calculations). Also, good industry practice for control charts is to show when data is missing as well, which is why the label for hidden and excluded rows will still exist. It shows that data is missing.
Dan Obermiller