The idea is still valid though. it just doesn't replace checks after the data entry.
break up the task

Ensure each new array is internally consecutive

easiest to do at data entry, when you don't have to think about all the other arrays

all the arrays together should hold 0 to #, and no number apears more than once.

after data entry. join the arrays, and sort it, as you are doing now

It adds a step, but doen't add much complexity.

This is assuming that the data is entered within 2 loops, that you can have the the check reset. something like:

my %list;
for my $outer=(1..5){
my $last=0;
for my $inner=(0..9){
my $number=<STDIN>;
unless ($last==0) {
unless ($number==$last+1){
die("bad input");
}
$list{$outer}[$inner]=$number;
}
}
[download]

Course its very rough code (and probably won't work without tweaking {or a total rewrite}) the principal is there.