double otherNumber = [self.labelTwo.text doubleValue];
You never want to use the view that displays the results as the storage for your data. That's a violation of the MVC paradigm, and just generally a poor plan. You should have the number in the display stored in your data model (even if that "model" is as simple as an instance variable in your view controller). Among other benefits, this avoids the need to convert the number to text and then back to a number, and therefore entirely avoids the problem you're having with commas.
Taking a look at the direct cause of the problem, you're using NSString's -doubleValue
method to convert from string to number, but using the number formatter to convert from number to string. As you've seen, the two aren't exactly complementary. Use the number formatter for both conversions and you'll have better luck. But, again, you really shouldn't be using the view to hold the operand.