The problem is that the window in which pywhatkit opens Whatsapp Web is not selected. When it opens Whatsapp Web, waits for a few seconds and clicks 'enter', the 'enter' is not processed by the browser window. Add the following code to your program:
# Import Libraries
import pywhatkit
import pyautogui
from tkinter import *
win = Tk() # Some Tkinter stuff
screen_width = win.winfo_screenwidth() # Gets the resolution (width) of your monitor
screen_height= win.winfo_screenheight() # Gets the resolution (height) of your monitor
print(screen_width, screen_height) # prints your monitor's resolution
pywhatkit.sendwhatmsg("+91xxxxxxxxxx", "Enter Message", 0, 0) # Sends the message
pyautogui.moveTo(screen_width * 0.694, screen_height* 0.964) # Moves the cursor the the message bar in Whatsapp
pyautogui.click() # Clicks the bar
pyautogui.press('enter') # Sends the message
No matter what screen you are using, pyautogui will always send your message except if Whatsapp updates its UI. In case this happens, then check where the message bar is located through pyautogui and whatever values you get, divide it by your screen's resolution. This way, it will work on any monitor.