Skipping Scheduled Auto-Messages Isn't The Same As Skipping Manual Messages, But It's Still Possible

To do this, filter for your Scheduled emails (either from the Emails page or from the Emails tab of a given sequence), select the ones you want to skip, and then click the 'Delete' button that appears -

This will then bring up the modal shown below -

From here, you can choose to either finish the sequence for the contacts being messaged (if the messages are in a sequence), or simply skip the messages you've selected. 

Important Note: You cannot undo either action, so be careful to select the correct one.