User Warning: Your stop_words may be inconsistent with your preprocessing

I am following this document clustering tutorial. As an input I give a txt file which can be downloaded here. It's a combined file of 3 other txt files divided with a use of \n. After creating a tf-idf matrix I received this warning:

,,UserWarning: Your stop_words may be inconsistent with your preprocessing. 
Tokenizing the stop words generated tokens ['abov', 'afterward', 'alon', 'alreadi', 'alway', 'ani', 'anoth', 'anyon', 'anyth', 'anywher', 'becam', 'becaus', 'becom', 'befor', 'besid', 'cri', 'describ', 'dure', 'els', 'elsewher', 'empti', 'everi', 'everyon', 'everyth', 'everywher', 'fifti', 'forti', 'henc', 'hereaft', 'herebi', 'howev', 'hundr', 'inde', 'mani', 'meanwhil', 'moreov', 'nobodi', 'noon', 'noth', 'nowher', 'onc', 'onli', 'otherwis', 'ourselv', 'perhap', 'pleas', 'sever', 'sinc', 'sincer', 'sixti', 'someon', 'someth', 'sometim', 'somewher', 'themselv', 'thenc', 'thereaft', 'therebi', 'therefor', 'togeth', 'twelv', 'twenti', 'veri', 'whatev', 'whenc', 'whenev', 'wherea', 'whereaft', 'wherebi', 'wherev', 'whi', 'yourselv'] not in stop_words.
  'stop_words.' % sorted(inconsistent))". 

I guess it has something to do with the order of lemmatization and stop words removal, but as this is my first project in txt processing, I am a bit lost and I don't know how to fix this...

import pandas as pd
import nltk
from nltk.corpus import stopwords
import re
import os
import codecs
from sklearn import feature_extraction
import mpld3
from nltk.stem.snowball import SnowballStemmer
from sklearn.feature_extraction.text import TfidfVectorizer


stopwords = stopwords.words('english')
stemmer = SnowballStemmer("english")

def tokenize_and_stem(text):
    # first tokenize by sentence, then by word to ensure that punctuation is caught as it's own token
    tokens = [word for sent in nltk.sent_tokenize(text) for word in nltk.word_tokenize(sent)]
    filtered_tokens = []
    # filter out any tokens not containing letters (e.g., numeric tokens, raw punctuation)
    for token in tokens:
        if re.search('[a-zA-Z]', token):
            filtered_tokens.append(token)
    stems = [stemmer.stem(t) for t in filtered_tokens]
    return stems


def tokenize_only(text):
    # first tokenize by sentence, then by word to ensure that punctuation is caught as it's own token
    tokens = [word.lower() for sent in nltk.sent_tokenize(text) for word in nltk.word_tokenize(sent)]
    filtered_tokens = []
    # filter out any tokens not containing letters (e.g., numeric tokens, raw punctuation)
    for token in tokens:
        if re.search('[a-zA-Z]', token):
            filtered_tokens.append(token)
    return filtered_tokens


totalvocab_stemmed = []
totalvocab_tokenized = []
with open('shortResultList.txt', encoding="utf8") as synopses:
    for i in synopses:
        allwords_stemmed = tokenize_and_stem(i)  # for each item in 'synopses', tokenize/stem
        totalvocab_stemmed.extend(allwords_stemmed)  # extend the 'totalvocab_stemmed' list
        allwords_tokenized = tokenize_only(i)
        totalvocab_tokenized.extend(allwords_tokenized)

vocab_frame = pd.DataFrame({'words': totalvocab_tokenized}, index = totalvocab_stemmed)
print ('there are ' + str(vocab_frame.shape[0]) + ' items in vocab_frame')
print (vocab_frame.head())

#define vectorizer parameters
tfidf_vectorizer = TfidfVectorizer(max_df=0.8, max_features=200000,
                                 min_df=0.2, stop_words='english',
                                 use_idf=True, tokenizer=tokenize_and_stem, ngram_range=(1,3))

with open('shortResultList.txt', encoding="utf8") as synopses:
    tfidf_matrix = tfidf_vectorizer.fit_transform(synopses) #fit the vectorizer to synopses

print(tfidf_matrix.shape)

I faced this problem because of PT-BR language.

TL;DR: Remove the accents of your language.

# Special thanks for the user Humberto Diogenes from Python List (answer from Aug 11, 2008)
# Link: http://python.6.x6.nabble.com/O-jeito-mais-rapido-de-remover-acentos-de-uma-string-td2041508.html

# I found the issue by chance (I swear, haha) but this guy gave the tip before me
# Link: https://github.com/scikit-learn/scikit-learn/issues/12897#issuecomment-518644215

import spacy
nlp = spacy.load('pt_core_news_sm')

# Define default stopwords list
stoplist = spacy.lang.pt.stop_words.STOP_WORDS

def replace_ptbr_char_by_word(word):
  """ Will remove the encode token by token"""
    word = str(word)
    word = normalize('NFKD', word).encode('ASCII','ignore').decode('ASCII')
    return word

def remove_pt_br_char_by_text(text):
  """ Will remove the encode using the entire text"""
    text = str(text)
    text = " ".join(replace_ptbr_char_by_word(word) for word in text.split() if word not in stoplist)
    return text

df['text'] = df['text'].apply(remove_pt_br_char_by_text)

I put the solution and references in this gist.