You're invoking the shell, and those characters have special meaning to your shell.

$ echo some_command a={1,2},{3,4}
some_command a=1,3 a=1,4 a=2,3 a=2,4
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You need to pass a shell literal that produces the desired arg, not the arg itself.

$ echo some_command 'a={1,2},{3,4}'
some_command a={1,2},{3,4}
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sub text_to_sh_literal {
   my ($s) = @_;
   s/'/'\\''/g;
   return "'$s'";
}

my $arg_lit = text_to_sh_literal($arg);
`some_command $arg_lit`
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You could also avoid the shell.

open(my $fh, '-|', 'some_command', $arg);
<$fh>
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