IDERA SQL Schema Compare exposes a wide variety of options to let you tweak the way the comparison engine works. From ignoring white spaces to performing automated file group translation you have control over it all. The default options have been carefully selected to match the most common scenarios however, every SQL Server implementation is different and there is no "one size fits all" scenario.
When an object is found to be different by the comparison engine while you believe it should be equal, or the other way around, don't panic - investigate the differences and carefully review those options - more likely than not one of those options holds the answer to your surprise.
Rule of thumb: whenever you are not sure what options would be better for your scenario, click Restore Default Options.