It would help to have specific examples of textbooks or courses that associate the Mughals with the medieval period, but the article "Early Modern India and World History" (Richards, 1992) argues that the Mughals should in fact be seen as part of the early modern period:
For South Asian history I believe it makes a good deal of sense to use the term early modern instead of Mughal India, or late medieval India, or late precolonial India for the sixteenth through the eighteenth centuries. To do so would lessen the extent to which India is seen as exceptional, unique, exotic, and somehow detached from world history. I am convinced that we must contextualize South Asian culture, civilization, and society in this way to better understand the more specific unfolding of Indian history in the sixteenth, seventeenth, and eighteenth centuries.
It goes on to outline that larger context in terms of "six distinct but complementary large-scale processes define the early modern world.":
- "the creation of global sea passages that came to link all of
humanity with a transportation network of increasing capacity and
- "the rise of a truly global world economy in which long-distance commerce, growing rapidly, connected expanding
economies on every continent.
- the growth, around the world, of states and other large-scale complex organizations that attained size, stability, capacity,
efficiency, and territorial reach not seen since antiquity, if then.
Early modern states displayed impressive new abilities to mobilize
resources and deploy overwhelming force.
- "the doubling of world population during the early modern centuries."
- "the intensified use of land to expand production in numerous episodes of settler frontiers."
- "the diffusion of several new technologies: cultivation of New World crops, gunpowder, and printing and organizational responses to them throughout the early modern world."