As Roy Johnson correctly said, your first regex matches the same lines, your third matches. This doesn't happen, if you anchor the regex with /^.../ for the start of the line.
I would also do it like this to not match the second regex,when it's not appropriate:
if (my $hit= /^port-channel (\d+)$/ .. /^\s*$/) {
if ($hit == 1) {
$pc_name = $1;
next;
}
$Rec->{$pc_name}->{$1} = $2 if (m|(fc\d+/\d+)\s+\[(\w+)\]|); #line
+ 15
}
elsif (my $hit= /^interface port-channel (\d+)$/ .. /^\s*$/) {
if ($hit == 1){
$key = $1;
next;
}
$hash->{$key}->{$1} = $2 if (/switchport description To (\w+) ([\d
+\.]+)/); #line 18
}
s$$([},&%#}/&/]+}%&{})*;#$&&s&&$^X.($'^"%]=\&(|?*{%.+=%;.#_}\&"^"-+%*).}%:##%}={~=~:.")&e;`$_'`
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