Ember is not used to the nuances of colors in Equestria, she said as much when she first arrived.  
Also ponies can easily look similar to eyes that are not used to seeing ponies.

@Starswirl  
Well like I said, dragon wings stick out, while ponies tend to fold them in. Plus, pony wings aren’t the same shape as dragon wings either, it would not be as familiar to a dragon, thus more easily overlooked.

@Background Pony #C20A  
You’d think a winged species would take notice of wings more readily…

@RIG
 
Yeah, but Twilight doesn’t exactly fly a lot, so they stay on her sides a lot. And since her feathers are the same color as her fur, then at a glance it wouldn’t be hard to not notice their presence or absence. Dragon wings, on the other hand, kind of stick out more often than not, so if she was using wings as an indicator, she isn’t likely to notice if they aren’t actually open.

@Ryodraco  
That sounds about right. Ember is one of the most sensible dragons we’ve seen so far, and even though she knows she’s smart enough, she tends to fall back to the most uncomplicated solution.

@Ryodraco  
That’s probably the best in-universe explanation that can be assembled.

Well that’s the joke Twilight and Starlight are an knockoff of each other their appearance is slightly different but their personalities and cutiemarks are just about the same.

@Background Pony #990B  
I think it plays more into how dragons are presented as to quite an extreme not being analytical or detail-oriented. Not stupid exactly but very much preferring to think about things in simple ways. Ember may be more intellectual than the average dragon, but she still seems to tend to see “purple pony with sparkly cutie mark” and not bother to commit anything else to memory. I wonder if dragons even know that there are distinctions between earth ponies, unicorns, pegasi, etc. given they’ve only ever referred to ponies as “ponies.”
 
That and presumably until this episode Ember could probably count on one hand the number of ponies she had seen up close.

What Ember said sounds like something from Fame and Misfortune.
 
Do you think it was a line that was cut for time and was put in this episode instead because that sounded like something a fan would say?

@Vaidelot  
Stop being the voice of reason.

Well, from Ember’s point of view they probably do look the same. As we’ve seen before, MLP-verse Dragons are VERY differ in size and shape, much more than two average ponies do…

@Sene86  

 
It is kind of a joke on Twi and Star being very similar. I wouldn’t usually say ‘It’s just a joke, it doesn’t have to make perfect sense’, but I will in this case.

All you purple ponies look alike!

@edvd  
I could still tell the difference even without Twi having wings. Twilight is a deeper color of purple and Starlight is a much lighter shade.

@ApplejackFan204  
It’s a metaphor for people who believe stupid things and refuse to change their minds when presented with mountains of compelling evidence to the contrary. Consider it an add-on to the previous episode’s meta-commentary.

@ApplejackFan204  

 
At a glance you can see how that might happen.

How can Ember not tell the difference between an a pony with a horn and a a pony with a horn and wings?

Ember would have a point of not being able to tell them apart IF TWILIGHT DIDN’T HAVE WINGS!

geez ember way to be racist
 
purple pony lives matter

Ahhh racism. Even MLP is no longer safe from such subjects.