Shell Scripting unwanted '?' character at the end of file name

It sounds like your script file has DOS-style line endings (\r\n) instead of unix-style (just \n) -- when a script in this format, the \r gets treated as part of the commands. In this instance, it's getting included in $emplid and therefore in the filename.

Many platforms support the dos2unix command to convert the file to unix-style line endings. And once it's converted, stick to text editors that support unix-style text files.

EDIT: I had assumed the problem line endings were in the shell script, but it looks like they're in the input file ("$i".txt) instead. You can use dos2unix on the input file to clean it and/or add a cleaning step to the sed command in your script. BTW, you can have a single instance of sed apply several edits with the -e option:

emplid=$(grep -a "Student ID" "$i".txt  | sed '-e s/(Student ID:  //g' -e 's/)Tj//g' -e $'s/\r$//' )

I'd recommend against using sed 's/.$//' -- if the file is in unix format, that'll cut off the last character of the filename.

using the file command to detect if it is pure unix or mixed with DOS.

DOS file: ASCII text, with CRLF line terminators

Unix file is pure ASCII file.