5) the gel got contaminated on earth. or the mass spec is not definitive about the molecule in question.
I lean towards 5, and then 3 as a close second.
I would have agreed with you before I RTFA. The authors acknowledged contamination as a confounding factor, and tested for it by isotopic analysis of the C13:C12 ratio, where glycine from space is expected to have a greater amount of C13. This is precisely what they found, allowing them to conclude that the glycine did, in fact, come from the comet.
The mutated organism can still mate with his "normal" fellows and produce children. But how, at some point there appears a group of organisms so different that they can reproduce only within their own group? This is not a small change and I don't understand how it can happen to the whole group simultaneously.
That's just it, speciation occurs when a subset of the population is no longer able to mate with the remainder of the population. Four modes through which this can occur are nicely covered in the Wikipedia article on speciation.
The program isn't debugged until the last user is dead.