This probably occurred because a new data object was mistakenly added in the Model Explorer by clicking on the Add Data button. Clicking on the Add Data button will automatically create a new data object called "data". Consider deleting this object by going to the Model Explorer, searching the model for "data", clicking on the "data" object and selecting Cut.
After removing the "data" object, re-run Check Subsystem Compatibility.
Here is a quick explanation of what "machine-parented" data is (from the Stateflow User's Guide , page 7-9):
Machine-parented data is data that you define for a Stateflow machine, which is the collection of all Stateflow blocks in a Simulink model. The Stateflow machine is the highest level of the Stateflow hierarchy. When you define data at this level, every chart in the machine can read and modify the data. To ensure that Mealy charts do not access data that can be modified unpredictably outside the chart, do not use machine-parented data.