You can debug a malleable VI by converting the instance of the VI to a standard VI and then enabling debugging.

After you place a malleable VI on the block diagram and wire specific data types to the inputs and outputs, the malleable VI adapts to the wired data types. You cannot debug the instance VI with the wired data types directly because the instance VI is inlined and debugging is disabled. However, you can debug this instance VI by converting it into a standard VI.

Right-click the instance VI and select Convert Instance VI to Standard VI to convert the instance VI into a standard VI. The standard VI then replaces the instance VI on the block diagram and the front panel of the standard VI opens. The standard VI has debugging disabled initially, but you can enable debugging on it by completing the following steps.
  1. Select File»VI Properties»Execution.
  2. Disable the Inline subVI into calling VIs option.
  3. Enable the Allow debugging option and one of the reentrant execution options.