With respect to your code .add is an invalid syntax with a list, .append should be used here, and before removing we have to check whether the val is already present in the list. If it is present, then only we should remove it.

#!/bin/python3

import math
import os
import random
import re
import sys


class Multiset:
    def __init__(self):
        self.items = []
    def add(self, val):
        #adds one occurrence of val from the multiset, if any
        return self.items.append(val)
        pass
    def remove(self, val):
        # removes one occurrence of val from the multiset, if any
        if self.items.count(val) != 0:
            return self.items.remove(val)
        pass
    def __contains__(self, val):
        # returns True when val is in the multiset, else returns False
        return val in self.items
    def __len__(self):
        # returns the number of elements in the multiset
        return len(self.items)
if __name__ == '__main__':
    def performOperations(operations):
        m = Multiset()
        result = []
        for op_str in operations:
            elems = op_str.split()
            if elems[0] == 'size':
                result.append(len(m))
            else:
                op, val = elems[0], int(elems[1])
                if op == 'query':
                    result.append(val in m)
                elif op == 'add':
                    m.add(val)
                elif op == 'remove':
                    m.remove(val)
        return result

    q = int(input())
    operations = []
    for _ in range(q):
        operations.append(input())

    result = performOperations(operations)
    
    fptr = open(os.environ['OUTPUT_PATH'], 'w')
    fptr.write('\n'.join(map(str, result)))
    fptr.write('\n')
    fptr.close()