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No it not harmful per se. But if your perl is nothing but shell commands then your code belongs in a shell script.

Sometimes writing the perl equivalent to a simple shell command is not worth...

jim mcnamara has got it.
You are sometimes picking up nascent files just after they have been created and before they contain data (hence the strange permissions). You could equally have been...

To expand a lot on vbe and RudiC's posts:

Does the first cron job ALWAYS complete in less than two minutes? If cron starts another job after two minutes and the previous one is still running,...

Some suggestions for a rework of the script:

1. Stay away from the backticks! Instead of date2=`date +%Y%m%d` use date2="$(date +%Y%m%d)"

2. Use shell means wherever possible, it is way faster:...

have you added the first line to tell which shell you are running? like
#!/bin/sh

You're attempting to extract the substrings before you've read any records.
awk 'BEGIN {sum_a=0;sum_b=0; }
{
a=substr($0,389,3);b=substr($0,399,3)
printf"%d\t\t%d",a,b;
sum_a = sum_a+a;
sum_b =...