Others have pointed out how to make the behaviour conform to your expectations; but I wanted to point out that ‘fix’ may not be the right term, since Data::Dumper is correctly indicating to you that your $hashref->{test1} and $hashref->{test2} are not just 2 references to similar hashes, but literally the same hashref. You can demonstrate this to yourself:

$hashref->{test1}{temp}[0] = 456;
print $hashref->{test2}{temp}[0]; # => 456
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The reason that you don't get the desired behaviour when you eval the output of Dumper is that the eval happens “all at once”—when the ‘inner’ reference to $VAR1->{test1}{temp}[0] is being evaluated, $VAR1 doesn't yet have the value that it will have when the eval completes, so all you're doing is auto-vivifying it as a reference to a hash-of-hashes-of-arrays. Accessing the 0th entry of that innermost array makes sure that it exists, but doesn't assign it a value, so it comes out undef. The documentation for Data::Dumper warns of this (but, in my opinion, not very clearly), and mentions the solution that ikegami already gave:

The default output of self-referential structures can be evaled, but the nested references to $VARn will be undefined, since a recursive structure cannot be constructed using one Perl statement. You should set the Purity flag to 1 to get additional statements that will correctly fill in these references. Moreover, if evaled when strictures are in effect, you need to ensure that any variables it accesses are previously declared.