Find scrambled words within word list
I'm not a Python programmer but I would take this approach, as if I understand the problem correctly, it seems like an easy solution. Along side that I believe it makes us of the language features also.

#!/usr/bin/env python3

# open word files
wordlist = open("wordlist.txt", "r").read().split()
words = open("words.txt", "r").read().split() 

s = list()

# loop through scrambled words
for word in words:
    # break scrambled word into characters
    chars = sorted(list(word))
    # loop through comparison list
    for compare in wordlist:
        if sorted(list(compare)) == chars:
            s.append(compare)

# create comma separated list of words
print(",".join(s))


This works on the bases that we do not care for order, so an ordered list of each will be a good check.

I have not broken out of the inner loop, as it is unclear weather multiple words could match and all of those words should be returned or not.

This is untested, as stated, I'm not a Python programmer.