ignore_case on term reference fields that are normalized to titlecase produce two terms one lower and one titlecase.

So when creating new terms:

    $this->addFieldMapping('field_collections', 'collections');
    $this->addFieldMapping('field_collections:ignore_case')->defaultValue(TRUE);
    $this->addFieldMapping('field_collections:create_term')->defaultValue(TRUE);

Produced a new term for "Cars" and "cars" when I assigned "Cars" to the $row->collections in prepareRow() during a CSV import.

Turning off ignore_case fixed the issue. Likely it's normalizing to find the result but using the normalized value also for setting the term name.