General :: Head Adds Chars To End Of Each Line (Red Hat Enterprise)

I wrote a bash-script that splits each of many .sql-files into two parts by some condition using head utlity. After that I execute all the scripts in sqlplus, and in one or two of them I get an error: SP2-0042: unknown command ")" - rest of line ignored. If I open the file with vi, I can see that in the end of each line there's a "^M", which is treated as a single character. If I delete this character placed before the closing parenthesis, the scripts executes without any errors. In the initial script opened by vi there's no such characters. Is it a problem with the head utility or with something else? Of course, I cannot grep these special chars.