@Spiked Punch  
Well said

@Background Pony #F0FF  
Almost in “It’s about Time,” Twilight got scared when Rainbow Dash said there’s a mouse behind her.

@Background Pony #6419  
Everybody wins.

Spike at your Service sucked.
 
There, mystery solved.

Twilight has an irrational fear of Timberwolves.
 
There, mystery solved.

@Spiked Punch  
Not to mention that Twilight ran away from the dragon in “Owl’s Well that Ends Well” and the teenage dragons in “Spike’s Quest”, and was terrified of snakes (snakes!) in “Winter Wrap-Up”. Of course, OP was interested only in cherry-picking “evidence” to support a conclusion he’d already drawn (s3/Meriweather/SaYS sucks, most likely) and not in rationally thinking through the issue.

Oh for crying out loud, its like OP didn’t even bother using his friggin brain here:
 
-While Nightmare Moon she HAD to take on (as it was her mission) she only charged at her with the iNTENTION to teleport and trick her to grab the elements. She knew she couldn’t fight her 1on1.
 
-Twilight KNEW that bear was an Ursa MINOR, not Major. And Ursa Minors are, despite their size, technically still babies/kids, so she knew that by treating it like a baby, she could avoid a direct confrontation (that she would’ve lost).
 
-They were ALL scared shitless of the red dragon the whole episode. However, running away would just allow it to cover Ponyville in smoke for 100 years so that wasn’t an optoion. Even then, Twilight knew it would be suicide to try and fight it even together, so she tried negotiating with him. She did this because despite the little knowledge on dragons, she KNEWS they cab talk/be talked to and maybe understand reasons. They’re not mindless beasts like manticores, Ursas, etc.
 
-The Hydra doesn’t even need an explanation. They were running from it the whole time. This pic was taken out of context as Twilight isn’t facing it, but rather trying to save Spike. But she never tried to fight it because she knew it was hopeless.
 
-Cerberus was actually on Ponyville already, and not chasing them on some random forest/cave/etc. If she ran away, others could get hurt and homes would be destroyed. That being said, she looked kinad confident against it, which, coupled with the in-depth knowledge she seemed to have on it, leads me to think she actually knew the precise method to deal with it without a direct confrontation, just like she did with the Uera Minor.
 
-The Changelings are a non factor. We’ve seen they’re pathetically weak individually.
 
All in all, its reasonable for Twilight to run away from the Timberworlfs. They’re dangerous creatures and while fragile, she probably figured it wasn’t worth it trying to fight them and risking getting shred to pieces before one got her or her friends.
 
Seriously, its like people think Twilight is some kind of battlemage. She’s not. All through MLP we’ve SEEN that Pony magic is mostly defensive or objective-oriented, and not that offensive. So either Twi knows the precise method to the deal with a beast without having to engage it in battle, or she flees because she knows she most likely wouldn’t be able to overpower them offensively.

Can’t deny, this was one of the moments in Season 3 I didn’t like. And wouldn’t ya’ know? In one of my least favorite episodes.
 
Yeah, they really tried nerfing Twilight, didn’t they? First the figure-eight animals in Magic Duel, then this.
 
I know that having written her as a lower god PRIOR to the alicorn thing makes it hard to write in challenges or fears for her, but pretending it was never so ain’t how you do it either.

More? What more? Why do you assume their would be more? Or that they could reform from injury far worse then not being fully connected? If their is no proof one way or another, then you assume no, if I told you I had a nuclear warhead, and their was no proof either way, would you automatically assume I have a nuke? This is not how debates work.
 
Also how would they reform from burnt ash? And even if they did, then a strong wind would be all that it takes to kill them again.  
Or once again, do what Twilight did with the Ursa Minor, and toss it a couple hundred meters away!

I love how we are arguing whether or not they are immortal even though it is never and I do mean NEVER said in the show if they are. all we know is that if they are smashed they can reform. that says nothing about if there is a way to kill them. they could be both, they could still reform after being burned or squashed. it’s not shown if they can or they can’t. and hell, who says more can’t just come from the forest after them if they kill a couple? it’s best to just roll with what happened and not over think it.

Thanks for the correction of my spelling random grammar Nazi background pony.  
(Not a insult)

defiant =/= definite  
defiantly =/= definitely

They’re*

Their not immortal!  
They can reform from fully formed branches, if you crush them with enough force to turn them into mulch (not that much force, defiantly less then you need to levitate a Ursa Minor), they should stay dead.  
Or using a laser to set them on fire and burning them to ash, and if you really care about the forest that much, levitate them up into the air so they can’t set the forest on fire either.
 
Or she could have used her telekinesis to literally throw it deep into the forest!

Timberwolves are magic and immortal.  
Also, without them, Ponyville would become a ghost town in days (no more Zap Apples).

Twilight can lift the Ursa she can turn the Tiber wolf into wooden mulch with a telekinesis squeeze, or set it on fire with one of the laser beams she’s seen Celestia do (she only seen Celestia use dark magic once, and copied it perfectly, why not the laser?), or literally throw it a couple kilometers away like she did the Ursa.

Oh, this one’s gonna be fun.
 
1.All of equestria (let alone celestia) is in danger.
 
2.All of ponyville is under attack.
 
3.The dragon wasn’t hostile at that point. She wasn’t exactly brave once it was.
 
4.To be fair, it was just a distraction.
 
5.Ponyville in danger…let alone that it wasn’t nearly as dangerous as it looked (it behaved like a normal dog…complete with basic dog command obediance and chasing after a ball).
 
6.Equestria in danger…again. (Wait a sec, didn’t she lose that one?)
 
7.Everyone in danger very able to get away safely. And they’re never seen far from the forest.
 
And they regenerate. So yeah.

It’s the CGI, Twilight is powerless to stand against it!

The previous times Equestria or Ponyville was in danger (so she had to be extra brave) or didn’t actually fight the monster. Versus the changelings they were outnumbered, so now she knows when it’s better to run.

It’s the bad breath. Twilight has to draw the line somewhere.

Um, 3 wolves against one pony = not good odds. Not to mention immortal.

Timberwolves are immortal. What are you going to do, stay in its domain and fight forever?

Dammit Merriwether, andd you were doing so well…  
Then you fall back to Cliché Cartoon Plot # 353?

:Merriwether Williams:

Twi is afraid because the wolves are in 3d