How did we get both sub- and infra- prefixes?
It seems that both sub- and infra- are prefixes that mean "below", leading to their use in different words to provide a similar meaning. We even have some words that are the same apart from these prefixes whose meanings could conceivably be flipped, eg. subsonic and infrasonic, substructure and infrastructure.
Normally in cases like this, the prefixes come from different languages but in this case, they both etymologically come from Latin. How did this come to be? Why 2 different prefixes with the same meaning?
Solution 1:
The OED says that "infra-" was not a common adjective prefix in Latin:
representing Latin infrā adv. and prep. ‘below, underneath, beneath’ (in medieval Latin also ‘within’), used in numerous recent formations, chiefly adjectival.
This use of infra- is scarcely a Latin one, though infrāforānus ‘situated beneath the forum’ occurs in an inscription (Lewis and Short), and infrāmūrāneus ‘lying within the walls’ in Gregory of Tours (Du Cange). Its recent employment is after the analogy of other prepositions; it is regularly opposed to supra-, sometimes to super-: the second element ought strictly to be one of Latin origin; but it is not always so.
It's not that uncommon for a language to have multiple prepositions with similar or overlapping meanings; e.g. English has both "under" (which is cognate with infra, actually) and "beneath", or "over" and "above".
Solution 2:
Actually, infra- is more commonly used to mean "inside, within", though it is also used with the same connotation of sub- as explained in the following extract by the Grammarist:
As a prefix, sub- means that the modified word is underneath, below, or in some way less than something else. It can mean a lower level of classification or a smaller part of something bigger.
With one exception, sub- words do not use a hyphen inside the United States. Outside, including Canada, most sub- words use a hyphen in their official spellings.
Infra- is also an prefix that can mean below, but usually means inside or within.
With a few exceptions, whether the classification uses sub- or infra- seems to be largely a matter of preference for the scientist naming the category. One could assume (taking into account the risks in doing so) that perhaps in the distinct examples one word already existed when another was needed.
One example of a distinct difference is subsonic and infrasonic. Subsonic is an adjective describing things as moving slower than sound moves. It dates from the 1930s. Infrasonic is an adjective describing things as being related to a certain range of sound that humans can’t hear. It dates from the 1920s. In this example, infra- means below on a scale and sub- means less in a comparison.
Another example is infrastructure and substructure. Infrastructure is the basic needs for a civilization to function, also the framework or foundation of an organization or group. This term dates to the 1930s. Substructure is simply a supporting part of a building that is underneath something else. This term dates to the 1700s. In this example, infra- means within or inside and sub- means below.