X is a dataframe and can't be accessed via slice terminology like X[:, 3]. You must access via iloc or X.values. However, the way you constructed X made it a copy... so. I'd use values
# Importing the libraries
import numpy as np
import matplotlib.pyplot as plt
import pandas as pd
# Importing the dataset
# dataset = pd.read_csv('50_Startups.csv')
dataset = pd.DataFrame(np.random.rand(10, 10))
y=dataset.iloc[:, 4]
X=dataset.iloc[:, 0:4]
# Encoding categorical data
from sklearn.preprocessing import LabelEncoder, OneHotEncoder
labelencoder_X = LabelEncoder()
# I changed this line
X.values[:, 3] = labelencoder_X.fit_transform(X.values[:, 3])