mirc automatically adds a CRLF as the last line when it writes to the file, but I don't see why this is a problem since that last line is ignored (for example, $lines() does not include that last line). Anyway, if you want to remove the ending CRLF you can use /btrunc:
/btrunc file.txt $calc($file(file.txt) - 2)
You can also check if the file ends in CRLF:
//bread file.txt $calc($file(file.txt) - 2) 2 &a | if ($bvar(&a,1-) == 13 10) { do stuff }