File permission(s) is not changed when you copy a file to a system folder.
If you use custom build scripts to install anything (AUR comes to mind) you need to understand what they are doing as you can compromise your system if you don’t.
Unless you deliberately execute any of those files using sudo there should be nothing to worry about.
You could make sure the files are not executable by explicitly removing the exec bit.
Data files should never have the exec bit set.
But - before you venture into a chmod -x folder -R yo need to understand that folders need the exec bit to allow navigating the folder.
Ensure you are executing this inside the top folder containing the files and folders you copied
You may need - to set the owner and group - $USER:$USER is an environment variable holding your current user:group. If the files are copied from a mix of unknown users - below command can be executed with sudo -
WARNING never do this in a system folder e.g. /. Always limit to files and folders you have write access to - thus ONLY inside your $HOME
chown -R $USER:$USERfind . -type f | sudo xargs -d'\n' chmod 664 # file permisson to rw for user and group and ro for other find . -type d | sudo xargs -d'\n' chmod 775 # folder permission to rw for user and group and ro for other find . -type d | sudo xargs -d'\n' chmod +s # set defaults for new files in a folder to inherit the folder permission– All my files, from Windows, are executable - #16 by linux-aarhus
ALWAYS keep the use of sudo to a minimum and check scripts which require sudo as those will be executed with elevated privileges.