I know megafauna is not a very common word, while fauna is more so. Fauna is singular, defined as a group of animals. ex. "The African fauna is diverse".
Megafauna is the word defining all animals with body mass larger than a certain threshold (45kg, 100kg, etc), so in theory is still a group.
Following this logic, megafauna should be singular.
However in many prominent scientific publications, for example some articles in Science and Nature, you find megafauna used in the plural form. ex. "Megafauna are a major draw for tourists" or "megafauna are imperiled".
Checking online some dictionaries define it as plural and singular. Are these scientists grammatically "wrong" by using megafauna as a plural noun, or are they simply setting the standard for how a word should be used since language evolves and they are the most expert on the subject?
No, they are not wrong. They are simply using collective nouns in a way that you are unfamiliar with. This is called notional concord, or sometimes notional agreement. This happens all the time in English. That makes this question a stealth duplicate of “Are collective nouns always plural, or are certain ones singular?”
The OED says of megafauna that it can take plural concord as a collective noun:
Chiefly Palaeontology. With plural concord: large vertebrates, esp. the larger mammals; spec. those of a particular epoch or region. Also (with singular concord): a group, class, community, or list of such animals. Cf. microfauna n. 1.
Ecology. = macrofauna n.
This is no surprise.
The word fauna is a collective noun, which means it can take plural verbs but does not require them. Here are examples from Google Books:
Preliminary results suggest that the endemic spider fauna are confined to the intact natural forests in the south-west and the central highland region.
—The Fauna of Sri Lanka: Status of Taxonomy, Research, and Conservation
The law further defines protected, controlled and common aquatic fauna in terms of the three-category classification system established in the law on Aquatic Animals and Wildlife: protected aquatic fauna are classified as Category I; controlled …
—Review of statutory and customary law in the Xe Champhone Ramsar site
Sand fauna, silty-sand fauna, and silty-clay fauna are common to this zone.
—Ocean Dumping of Sludge in New York Bight: Environmental Impact Statement
This works just like uncountably many other collective nouns that are singular in form yet often plural in use: group, team, community, couple, pair, council, club, company, troop, crowd, gang, et cetera ad infinitum.