When using an 'Update List Item' action in Nintex Workflow for Office 365, to update a number field with the option show as percentage checked, the result is the input value is multiply by 100. 
Example: 
Input value : 100 
Result in SharePoint list : 10,000% 

This is an expected behavior as this can be replicated with SharePoint Designer. 

To avoid any confusion, Nintex has also updated the description for the "Update List Item" action in Nintex Workflow for Office 365 

The added description is: 
This item is configured to show as a percentage. Enter a value between 0 and 1. For example, enter .5 to show as 50%.