Actually it may not be helium at all. "Helium" word first appeared as Crichton's guess, because of contracted vocal cords (hence the funny vocal) and being odorless. Contraction is not a chemical process that defines a substance. His limited experience made him to presume that it is helium. In actuality, it may be a gas that has the same basic effect on humans as helium, but that can be generated through some biochemical process.
So, why it might be accepted and remained as being said helium? It might be because the TV audience is supposed to have the same translator microbes as Crichton.
The translator microbes may have translated it as a noun rather than an element name. So, the intermediate verbal object (that is, the low level language of microbes remained only between them, this is implicitly required by the exposed mechanism of microbes) between Crichton's microbes and the others is falsely related.