protocol_whitelist is a parameter only on the input file (in your case, MIE.m3u8), so it must be specified before the input in your command.
Specify -protocol_whitelist file,http,https,tcp,tls prior to -i and it’ll work as you expect:
ffmpeg -protocol_whitelist file,http,https,tcp,tls,crypto -i MIE.m3u8 -c copy -bsf:a aac_adtstoasc MIE.mp4
You can a similar case on a Debian Bugs discussion board, and read up more on the syntax of ffmpeg commands.