Update: Bah, I should head my own advice. The second statement never gets a chance to execute.

You're looking at the statements in isolation. Look at them as a pair.

Original post: (WRONG!)

# First time
next unless defined %{$matches{$fasta_id}};         # False
last unless defined @{$matches{$fasta_id}{$site}};  # False

# Second time
next unless defined %{$matches{$fasta_id}};         # Now true!!
last unless defined @{$matches{$fasta_id}{$site}};
[download]

What really happens:

# First time
next unless defined %{$matches{$fasta_id}};         # False -> next
last unless defined @{$matches{$fasta_id}{$site}};  # Skipped by next

# Second time
next unless defined %{$matches{$fasta_id}};         # Still false
last unless defined @{$matches{$fasta_id}{$site}};
[download]