How to stop pygame buttons from overlapping in separate images?

I’m making a simple text based RPG game in pygame. I’m using a button class (not mine, but fairly simple to use and integrate) to add buttons with choices in them. However, it seems a button on the second slide, the ‘Sit and Wait’ choice, is overlapping with the ‘No’ button on the first slide. Since the No button closes the game, pressing on Sit and Wait seems to close the game also. I’ve tried ordering the if-else statements in different ways, but every other button seems fine. Any tips? Thank you. Here is my code, sorry I know it’s a lot but I’m a beginner and not great at condensing yet:

import pygame
pygame.init()
win=pygame.display.set_mode((800,700))
win.fill((255,255,255))
our_game_display=pygame.Surface((800,700))
font_name = pygame.font.get_default_font()
class button():
    def __init__(self, color, x, y, width, height, text=''):
        self.color = color
        self.x = x
        self.y = y
        self.width = width
        self.height = height
        self.text = text
    def draw(self, win, outline=None):
        # Call this method to draw the button on the screen
        if outline:
            pygame.draw.rect(win, outline, (self.x - 2, self.y - 2, self.width + 4, self.height + 4), 0)
        pygame.draw.rect(win, self.color, (self.x, self.y, self.width, self.height), 0)
        if self.text != '':
            font = pygame.font.SysFont('comicsans', 30)
            text = font.render(self.text, 1, (255, 255, 255))
            win.blit(text, (self.x + (self.width / 2 - text.get_width() / 2), self.y + (self.height / 2 - text.get_height() / 2)))
    def isOver(self, pos):
        # Pos is the mouse position or a tuple of (x,y) coordinates
        if pos[0] > self.x and pos[0] < self.x + self.width:
            if pos[1] > self.y and pos[1] < self.y + self.height:
                return True
        return False
def draw_text(text, size, x, y):
        pygame.font.init()
        font = pygame.font.Font(font_name, size)
        text_surface = font.render(text, True, (255,255,255))
        text_rect = text_surface.get_rect()
        text_rect.center = (x, y)
        our_game_display.blit(text_surface, text_rect)
def yell_choice():
    our_game_display.fill((0, 0, 0))
    draw_text('You yell to see if anyone can hear you.', 20, 800 / 2, 700 / 2 - 100)
    win.blit(our_game_display, (0, 0))
    pygame.display.update()
def sit_choice():
    our_game_display.fill((0,0,0))
    draw_text('So you decided to sit and wait', 20, 800 / 2, 700 / 2 - 100)
    win.blit(our_game_display,(0,0))
    pygame.display.update()
def search_choice():
    our_game_display.fill((0,0,0))
    draw_text('So you decided to search', 20, 800 / 2, 700 / 2 - 100)
    win.blit(our_game_display,(0,0))
    pygame.display.update()
def beginning_question():
    our_game_display.fill((0, 0, 0))
    draw_text('The story of this game depends on your choices. Do you wish to play?', 20, 800 / 2, 700 / 2 - 100)
    win.blit(our_game_display, (0, 0))
    YesButton.draw(win, (255, 255, 255))
    NoButton.draw(win, (255, 255, 255))
    pygame.display.update()
def begin_game():
    our_game_display.fill((0,0,0))
    draw_text("You wake up, or...at least you think you do. Even though your eyes are open,", 20, 800 / 2, 700 / 2 - 300)
    draw_text("they still can't detect anything in the complete darkness that surrounds you.", 20, 800 / 2, 700 / 2 - 270)
    draw_text("What do you do?", 20, 800 / 2, 700 / 2 - 210)
    win.blit(our_game_display,(0,0))
    SitWaitButton.draw(win,(255,255,255))
    SearchButton.draw(win,(255,255,255))
    YellHelpButton.draw(win,(255,255,255))
    pygame.display.update()
#game loop
running = True
#color,x,y,width,height
YesButton=button((0,0,0),100,500,250,100,'Yes')
NoButton=button((0,0,0),450,500,250,100,'No')
SitWaitButton=button((0,0,0),500,500,200,50,'Sit and wait..')
SearchButton=button((0,0,0),250,600,600,50,'Get up and try to search your surroundings.')
YellHelpButton=button((0,0,0),250,400,600,50,'Yell to see if anyone is there.')
game_begun='Input' #beginning choice variable
search_option='Input'#search variable
sit_option='Input' #sitting variable
yell_option = 'Input'
while running:
    if search_option=='Go':
        search_choice()
    elif sit_option=='Go':
        sit_choice()
    elif yell_option=='Go':
        yell_choice()
    elif game_begun=='Go':
        begin_game()
    else:
        beginning_question()
    for event in pygame.event.get():
        pos=pygame.mouse.get_pos()
        if event.type==pygame.QUIT:
            running = False
            pygame.quit()
            quit()
    #yes and no buttons for beginning question
        if event.type==pygame.MOUSEBUTTONDOWN:
            if SitWaitButton.isOver(pos):
                sit_option = 'Go'
                print("this button is working")
            if SearchButton.isOver(pos):
                search_option = 'Go'
                print("this button is working")
            if YellHelpButton.isOver(pos):
                yell_option='Go'
                print("this button is working")
            if YesButton.isOver(pos):
                game_begun='Go'
            if NoButton.isOver(pos):
                running=False
                pygame.quit()
                quit()
        if event.type==pygame.MOUSEMOTION:
            if YellHelpButton.isOver(pos):
                YellHelpButton.color = (0, 0, 139)
            elif SitWaitButton.isOver(pos):
                SitWaitButton.color = (0, 0, 139)
            elif SearchButton.isOver(pos):
                SearchButton.color = (0, 0, 139)
            elif YesButton.isOver(pos):
                YesButton.color=(0,0,139)
            elif NoButton.isOver(pos):
                NoButton.color=(0,0,139)
            else:
                YesButton.color=(0,0,0)
                NoButton.color=(0,0,0)
                YellHelpButton.color = (0, 0, 0)
                SitWaitButton.color = (0, 0, 0)
                SearchButton.color = (0, 0, 0)

Answer

You can use an if-elif instruction like below, so that if the user clicks on the mouse while cursor is over the sit and wait button then you don’t check if it’s also over the quit button (and thus you don’t quit the game):

            if SitWaitButton.isOver(pos):
                sit_option = 'Go'
                print("this button is working")
            elif NoButton.isOver(pos):
                pygame.quit()
                quit()

A cleaner solution would however be to remember which buttons are actually currently displayed. For example, you could have a list of visible buttons and check if the cursor is over a button only if this one is in the list.

On a side note, your running variable is useless: your main loop is while running but as soon as running is set to False you just quit the game immediately. So the condition of your loop never evaluates to False.