The scientists throughout the movie are trying to access a vaccination to save themselves from the flu they are already sick with. Vaccinations for the flu must be given prior to infection; once a person is already sick, the vaccine will not help. The speech at the end of the movie also implies that the characters were saved by the vaccine.
The scientists, although they were attempting to make the most dangerous flu strain, did not use the most deadly strain. H1N1 is not the flu strain with the highest mortality in humans.
The characters repeatedly show symptoms that are not associated with any strain of the flu, such as coughing up blood.
One of the characters gives a speech in which they talk about when H1N1 first appeared in humans. They talk about this as if it happened within very recent history, when in fact the first appearance of H1N1 was centuries ago.
The characters at times say they are looking for an antidote. Antidotes are for poisons and toxins, not for viral infections.