These Replica soldiers only appear while moving through the Armacham Technology Corporation access tunnel underneath Fairport, in the second-to-last level of Project Origin. It is possible that these Replicas were deployed in an emergency to stop Dark Signal from reaching Still Island and were simply not fully equipped when encountered. This is supported by the fact that Michael Becket only encounters them while moving through an ATC storage facility, and the deformed Replicas only appear after emerging from their stasis pods.
Deformed Replicas have deformed faces, indicative of their cloned nature, either showing that ATC's cloning process is imperfect or that these clones were prematurely developed. This possibly explains why they are amongst the weakest of the Replica forces. In addition, these Replicas snarl and grunt madly, despite their advanced combat technique. The disturbing nature of their faces and distorted vocalizations may indicate that the reason why the Replicas universally wear face-concealing masks and speak with electronically-modified voices is to hide their inhuman nature from the casual observer. However, it is also possible that their gruesome appearance was due to inadequate gestation in the cloning process.