How to bulk rename files and remove additional characters after extension in linux

If you want to rename the existing files, please try:

#!/bin/bash

for f in *mp4$'\r'; do
    mv -- "$f" "${f%$'\r'}"
done

It assumes the *mp4 files are located in the same directory. If you want to fix the filenames in the current directory recursively, please try:

#!/bin/bash

shopt -s globstar
for f in **/*mp4$'\r'; do
    mv -- "$f" "${f%$'\r'}"
done

BTW if you want to fix the filenames downloading from now on, modify your awk command as:

awk '{url=$1; $1="";{sub(/ /,""); sub(/\r$/, "");out=url" -O \""$0"\""}; print out}' file.txt | xargs -L 1 wget

It removes the trailing CR characters out of the names in file.txt then passes the corrected filenames to wget.