You're not showing us the relevant code. What is line 90? Get rid of all the code you don't need, and add just the relevant code which demonstrates your problem (http://sscce.org).

When I add this to the top of your code

use Getopt::Long;

getCmndArg();
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and run it, I get:

program.pl --help --dfiles --err_dup F68 F100 5
help is called - Help Panel:
dfiles is called - deleting old simulation files
err_dup is called
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