I know this post is 5 years old, but I had the exact same question... Rachel isn't sitting so I don't know if the "scrunched up" theory works here. In this context, I would say it's something similar to "moody", but I guess it's not a common expression. I would love to hear new theories
Scrunchy does not seem to be usually used in this way. But Merriam-Webster’s definition 2c of SCRUNCH as a transitive verb is: to cause (something, such as one’s features) to draw together — usually used with up.
This tends to support Owlman’s 5-year-old guess in #2.
OED also supports Owlman's idea, by recognizing the adjective scrunchy not only as "something that scrunches or emits a crisp, crunching sound when crushed", but also, in its draft additions 2011, as "of a wrinkled or ruffled appearance".
There are even some face-related citations:
1933 Indiana (Pa.) Progress 8 Mar. 4/4 Her eyes had looked all scrunchy when she told him.
2009 C. Martinusen-Coloma Ruby Unscripted iv. 36 Aunt Jenna does that little scrunchy face she gets when trying to tell me something without hurting my feelings.
Phoebe is the odd one so it could be Phoebe-speak and nothing so specific.
So I just watched it. It starts about 2:45 from the beginning.
The odd thing is that while Rachel is clearly aggravated with Ross (but actually mad at her father, which is causing her to be in a bad mood) she doesn't actually scrunch up her face at all. Almost the opposite. She just taps her pen in exasperation and casually stares at him. But when Phoebe asks the question, Phoebe does scrunch up her own face (and her hands, too). So I think Phoebe is using it semi-figuratively to mean "Why are you in such a bad mood?"