@moonlightaveger  
Yeah, I’m just providing plausible reasons why she seemed confused.

@Amethyst_Crystal  
Thinking back on it, there are a lot of ‘ifs involved. I did think of Philomena as a normal pet and I was probably wrong doing that. Though Twilight has an owl (not really ‘normal’) for pet and Pinkie has a… Gummy. On later episodes we learn that ponies can have two-headed dogs for pets. I’m not convinced that phoenixes as pets, or in the wild, are that rare.
 
Later seasons Fluttershy has shown that she knows about such creatures, the two-headed dog for example, that she identifies; and also talks about breezies and is known enough to be allowed to observe breezies by the Equestrian Society for the Preservation of Rare Creatures.
 
I’m inclined to believe that she should know what is a phoenix. In a similar way a doctor is expected to identify rare diseases and conditions by the simple fact of being a doctor. The point is that magical creatures are common place in Equestria.
 
But, there is a lot of assumptions anyway and it’s not like MLP cares about that.

@moonlightaveger  
@ZeroSpawn47  
I think way back in season 1, it didn’t seem as much of a mistake on Fluttershy’s part,  
because she mostly seemed to specialize in normal animals,  
(and maybe just guessed intuitively about the manticore in the premiere).
 
She has shown to know about all kinds of magical creatures nowadays,  
but perhaps she was inspired to learn more after this ‘phoenix incident’.
 
It could also be that Celestia doesn’t take her pet phoenix out in public much,  
and keeps Philomena more of a personal secret: an immortal pet to keep her company.
 
I wonder how long they’ve known each other…

@TheAntiCat  

 
Well yes, but if we’re taking it completely seriously (and it’s really not meant to be taken this seriously), there’s just too much we don’t know. Has Celestia allowed ornithologists to study Philomena? How common is the study of phoenixes? If studies have been done, you’d think there would be books detailing the phoenix cycle. But, how common are those books? Does Ponyville’s library have any? Has Fluttershy ever had the opportunity to read those books? Also, is the fact that Celestia has a pet phoenix common knowledge? There are probably more questions of this nature.  
The answer only has to be “no” to one of these questions for it to be reasonable for her not to know.

@TheAntiCat  
I didn’t say that she has to know everything. I said that she should know what a phoenix is, considering it’s the princess’ pet. If Fluttershy saw a dragon, she’d know it’s a dragon. A phoenix, is not a dragon, and a dragon, being a creature ponies know little of, can be identified by it’s general characteristics. Considering the cycle of death and rebirth is a characteristic of a phoenix, and that they exist in that world, then identifying a phoenix should relatively easy.
 
Now, let me help you people with something. Here is what I said:“It’s a shame the animal expert doesn’t know what the hell a phoenix is. I don’t know who was worse in that episode. XD”
 
Here is how to properly interpret it: “LOL. Fluttershy doesn’t know it’s a phoenix, Celestia is being Celestia, Twilight is being Twilight and that bird is a jerk. Ha ha. It’s funny.”
 
Here is how not to interpret it: “Holy shit! Fluttershy is suck a hack! How can she not know it’s a phoenix!? Fluttershy sucks! Her fans suck! They should be ashamed that she doesn’t know it’s a phoenix. OMFG! Fluttershy is the worst character in the show and her fans should be sad! This is serious! So serious that PETA should publish a report about how awful this cartoon is for making fun of phoenix experts all over the universe!!!11one”

@moonlightaveger  
Expert =/= all-knowing
 
The show has stated that ponies know very little about dragons. How many other creatures are they lacking in knowledge of or outright ignorant of?

@ZeroSpawn47  
It depends. Is there a species or group of species where that happens as part of their normal cycle? Then yes.

@moonlightaveger  
Is it normal for animal experts to be able to distinguish birds from each other when they have no feathers?

It’s a shame the animal expert doesn’t know what the hell a phoenix is. I don’t know who was worse in that episode. XD

“Philomena my pet is a phoenix”  
“I love Philomena :)”  
END