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As programming projects grow bigger and time grows shorter things can often get messy. The Evolution project was basically coded and shrink-wrapped in a single week. Likely, bugs are hiding away in the more unpolished parts of the code.
One of the more interesting bugs was uncovered when the creatures that spawned from the factory started running wild. Things with a single flipper or two heads were happily reproducing in the background memory. Look at the creature below: it has the tentacles of one of its ancestors but they got positioned all wrong. Moreover, the thing has grown some extra tentacles of another type!
We never defined a sort of symmetry in the genetic recombination code, so when two ancestors were mixed of which one had four flippers and the other two, three flippers became an option for the child. Since the factory code didn't know how to handle an uneven amount of flippers, it started attaching them to the wrong places and adding other stuff to fill in the gaps in the DNA.
It's very hard to check the programming code for these kinds of things... evolution can't be constrained it seems!