my $line ;
my (%resultarray,$part1,$part2);
my @AoH=();

while($line = <FILE>) {

    ...

    push @AoH, \%resultarray;
}
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You have declared %resultarray in file scope so that the reference always refers to the same variable.    You have to declare your variables in the smallest possible scope:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

open my $FILE, '<', 'temp' or die "can not open temp $!";

my @AoH;

while ( my $line = <$FILE> ) {
    chomp $line;
    my ( $part1, $part2 ) = split /#/, $line;

    my @resultarry2 = split /\s/, $part1;

    my %resultarray = (
        split( /[=;]/, $part2 ),
        datetime => "@resultarry2[ 1, 2 ]",
        threadname => $resultarry2[ 6 ]
        );

    push @AoH, \%resultarray;

}
close $FILE;

my $numberofhashes = @AoH;
print "$numberofhashes\n";
my $hr2 = \@AoH;
print Dumper $hr2;
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Or even just:

#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

open my $FILE, '<', 'temp' or die "can not open temp $!";

my @AoH;

while ( my $line = <$FILE> ) {
    chomp $line;
    my ( $part1, $part2 ) = split /#/, $line;

    my @resultarry2 = split /\s/, $part1;

    push @AoH, {
        split( /[=;]/, $part2 ),
        datetime => "@resultarry2[ 1, 2 ]",
        threadname => $resultarry2[ 6 ],
        };

}
close $FILE;

print scalar( @AoH ), "\n";

print Dumper \@AoH;
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