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I assume you mean when it hits the true path here?

[code]if (isset($this->entities[$class][$primary]))[/code]

If so, then no, that would be expected. There should only ever be one instance of a given entity at a time (at least that's attached). This means that if changes happen (or are pending), they are reflected in all places that reference that entity (given PHP's passing object by reference), including any new instantiation requests.