To solve this issue, you can use to perform metabolization on the "Profiling" tab instead of the "Input" tab. This will produce an output on the main screen, under the profiling node instead of the left pane. 


After applying the desired simulator or observed metabolism, just expand the Profile>>Metabolism/Transformations>>"Applied simulator" on the main screen and you can simply double click in order to search or export to a .smi file all the created metabolites.