Middle Indo-Aryan resolved a large class of inherited clusters by assimilating them into doubled consonants, and where the cluster contained a retroflex element and an aspirate the outcome was frequently this sound written twice over. Brahmi writes a doubled consonant as a conjunct like any other cluster, the second copy stacked beneath the first, so the sign occupies two levels of the writing space rather than appearing twice side by side.
That vertical stacking is one of the defining habits of the script and it has consequences a reader notices immediately. A line of Brahmi is not a strip of equal-sized signs but a band with material hanging below it and marks sitting above it, and a cluster of three consonants with a vowel mark can occupy a good deal of vertical room. The descendant scripts handle this in different ways: some kept the stacking and became famously three-dimensional on the page, some flattened the clusters into horizontal ligatures, and some, in Southeast Asia, developed subscript forms of every consonant as a regular part of the system. Which route a script took is one of the ordinary ways of grouping the family.
Doubling has a second consequence, in metre rather than in writing. A syllable followed by a cluster is heavy whatever its own vowel, and a doubled consonant is a cluster, so the Middle Indo-Aryan assimilation that produced these doubles also changed the metrical shape of the words involved. Prakrit verse and Sanskrit verse therefore scan differently even where the vocabulary corresponds word for word, and a reader working out the metre of an inscription has to know which stage of the language is in front of them.