Do you sent a Word document or an ePUB to Smashwords? If it is the first, it will be difficult. They have a program called Meatgrinder that destroys you Word document and tries to make a ePUB out of it.
If you sent an ePUB and FlightCrew and the validator online give no warnings, it should be fine structure wise. However, what might be important is knowing which version of the validator Smashwords use. Probably an old version with bugs that were fixed in a later version.
The message indicates that there is a problem with a reference. That could be either a bookmark or perhaps in the ncx file. You can try searching for: /Text/"
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