Learn@UW - Warnings Issued for Unanswered Questions in Branching Surveys
After answering the questions presented in a branching survey, when you reach the end and press Submit, you are issued a warning regarding the unanswered questions.
Since branching intentionally skips over the irrelevant questions, this can be misleading.
When you receive the warnings regarding the unanswered questions, press Submit again. Then respond Yes to "Are you sure that you want to submit the survey with unanswered questions?".
This is a known issue.