That's a feature of XML::Simple - this difference of behavior between a node which happens once or multiple times. Most of the time, when you expect a node that happen one or more times, you want to tell XML::Simple to always return an array of hashes, so you have a uniform way to deal with the data.

That's what ForceArray attribute for.

$data = XMLin( $xml, ForceArray => [ qw(Layer) ] )
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Otherwise you'll always have to code something like that:

my $layers = $data->{Capabilities}->{Layer};
for my $layer ( ref $layers eq 'ARRAY' ? @$layers : ( $layers ) ) {
    # do something to each Layer
}
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