I have a clear command which deletes the amount of messages you would like to. But whenever I say clear 3, it'll clear only 2 messages instead.
client.on('message', async (message) => {
  if (
    message.content.toLowerCase().startsWith(prefix + 'clear') ||
    message.content.toLowerCase().startsWith(prefix + 'c ')
  ) {
    if (!message.member.hasPermission('MANAGE_MESSAGES'))
      return message.channel.send("You cant use this command since you're missing `manage_messages` perm");
    if (!isNaN(message.content.split(' ')[1])) {
      let amount = 0;
      if (message.content.split(' ')[1] === '1' || message.content.split(' ')[1] === '0') {
        amount = 1;
      } else {
        amount = message.content.split(' ')[1];
        if (amount > 100) {
          amount = 100;
        }
      }
      await message.channel.bulkDelete(amount, true).then((_message) => {
        message.channel.send(`Bot cleared \`${_message.size}\` messages :broom:`).then((sent) => {
          setTimeout(function () {
            sent.delete();
          }, 2500);
        });
      });
    } else {
      message.channel.send('enter the amount of messages that you would like to clear').then((sent) => {
        setTimeout(function () {
          sent.delete();
        }, 2500);
      });
    }
  } else {
    if (message.content.toLowerCase() === prefix + 'help clear') {
      const newEmbed = new Discord.MessageEmbed().setColor('#00B2B2').setTitle('**Clear Help**');
      newEmbed
        .setDescription('This command clears messages for example `.clear 5` or `.c 5`.')
        .setFooter(`Requested by ${message.author.tag}`, message.author.displayAvatarURL())
        .setTimestamp();
      message.channel.send(newEmbed);
    }
  }
});
                Your code works fine, it deletes the correct number of messages. What you forgot is that your current message with the comment is also a message, and will also count towards the amount deleted. So you can increase this number by one.
I would probably make some changes to your code:
.clear  5. If you check, isNaN(' ') is false.prefixes.await.prefix.client.on('message', (message) => {
  if (!message.content.startsWith(prefix) || message.author.bot) return;
  const args = message.content
    .toLowerCase()
    .slice(prefix.length)
    .trim()
    .split(/\s+/);
  const [command, input] = args;
  if (command === 'clear' || command === 'c') {
    if (!message.member.hasPermission('MANAGE_MESSAGES')) {
      return message.channel
        .send(
          "You cant use this command since you're missing `manage_messages` perm",
        );
    }
    if (isNaN(input)) {
      return message.channel
        .send('enter the amount of messages that you would like to clear')
        .then((sent) => {
          setTimeout(() => {
            sent.delete();
          }, 2500);
        });
    }
    if (Number(input) < 0) {
      return message.channel
        .send('enter a positive number')
        .then((sent) => {
          setTimeout(() => {
            sent.delete();
          }, 2500);
        });
    }
    // add an extra to delete the current message too
    const amount = Number(input) > 100
      ? 101
      : Number(input) + 1;
    message.channel.bulkDelete(amount, true)
    .then((_message) => {
      message.channel
        // do you want to include the current message here?
        // if not it should be ${_message.size - 1}
        .send(`Bot cleared \`${_message.size}\` messages :broom:`)
        .then((sent) => {
          setTimeout(() => {
            sent.delete();
          }, 2500);
        });
    });
  }
  if (command === 'help' && input === 'clear') {
    const newEmbed = new MessageEmbed()
      .setColor('#00B2B2')
      .setTitle('**Clear Help**')
      .setDescription(
        `This command clears messages for example \`${prefix}clear 5\` or \`${prefix}c 5\`.`,
      )
      .setFooter(
        `Requested by ${message.author.tag}`,
        message.author.displayAvatarURL(),
      )
      .setTimestamp();
    message.channel.send(newEmbed);
  }
});
                        That's because it's deleting the message triggering it too. Simple fix, just take the number given, and add one to it.
await message.channel.bulkDelete(parseInt(amount) + 1, true).then((_message) => {
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