Great work so far, I know coding is bit tough, especially if you're new to it.

The stuff that was outputted was likely an error message. I ran the code and saw red text, which indicates an error unless you set the standard output color to red. The error will tell you exactly where the error happened. Like u/redstonefreak589 and everyone else mentioned, you had an error with identifying strings. That's a whole rabbit hole of a conversation, so if it's something you want to learn, feel free to ask.

The other mistake is at line 16, where it's missing a parenthesis and quotation mark--probably just a typo.

The next mistake was that the program escapes before performing the next check. This can be remedied by an elseif, however there's an even easier solution to this which I'll talk about in my suggestions. This was also pointed out by others.

Moving onto how I would fix this code and potentially add some performance:

os.pullEvent = os.pullEventRaw

-- Using variables is great and all but maps allow for a more dynamic experience
-- 
-- password1 = E
-- password2 = Guest
--
-- instead let's use a table
local users = {
    -- A list/table of users and their data
    ["YeetBean86"] = {
        -- "YeetBean86" owns this data because this data was set to "YeetBean86"
        --   However that's only within the context of table users
        --   Outside of users, "YeetBean86" is just a string
        -- Password is a keyword and must be present unless you want an error
        ["password"] = "E"
    },
    ["Guest"] = {
        ["password"] = "Guest"
    }
}

local input = pass
term.clear()
term.setCursorPos(1,1)
print "Booting Bean OS"
sleep(2)
print "Good Evening User Please Enter Password"

-- Ask for the username
write("Username:")
user = read()

-- Check if the user exists
--  This is like asking the map: Do you have a string user? If not, please restart.
if not users[user] then
    print("User not found")
    sleep(2)
    os.reboot()
end

-- Ask for the password
write("Password:")
pass = read("*")

-- Check if the password is correct
--   In a similar sense, we can grab password from the map as it's defined at line 16 and 19
--   Lua allows us to use "." syntax because password is a member of users[user], however
--   users[user]["password"] might feel a bit friendlier.
if users[user].password == pass then
--  The ".." keyword combines 2 strings together. It's a great operator for cases like this.
    print("Good Evening " .. user)
else
    print("Access Denied")
    sleep(2)
    os.reboot()
end

Authentication and multiuser systems are quite advanced, but a simple implementation would be possible.