It's got nothing to with while or with Moose. _wafer_parse is clobbering its caller's $_. Don't assign to a global variable without localising it first.

sub _wafer_parse {
    my $self = shift;
    
    open my $FILE, "<", $self->{file};

    local *_;
    while ( <$FILE> ) { ... }
}
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Better yet, don't assign to global variables.

sub _wafer_parse {
    my $self = shift;
    
    open my $FILE, "<", $self->{file};

    while ( my $line = <$FILE> ) { ... }
}
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