Why is the "I" in "Indigenous crisis" capitalized?

It's capitalized to indicate a specific group of people, i.e. the "Indigenous" Maori's. "Maori" also capitalized as to indicate their race of people are "Maori".

It's similar to the use of the words Aboriginal and Squatter in Australia.

The word aboriginal with a lower case 'a' means 'indiginous' or 'original inhabitant' but 'Aboriginal' with an upper case 'A' came to refer to people descended from the indigenous people of Australia {with all the attendant bias and abuse that accompanied colonialism}.

The word 'squatter' with a lower case 's' on the other hand means someone who occupies a property or piece of land either illegally or without legal title of any sort. However the word 'Squatter' with an upper case 'S' has come to mean a large, wealthy landowner. I understand that 'Squatter' meaning a landowner is often written with a lower case 's' but whenever 'Squatter' appears in the middle of a sentence it will refer to a large landowner, not a homeless person occupying a building illegally.

"Indigenous" is capitalized in that article because the author viewed it as a proper noun or adjective (both of which are capitalized in English).

Unfortunately, there aren't clear criteria for determining when a noun or adjective in English "counts as" a proper noun/adjective vs. common noun/adjective. You just have to learn how each word is used. (Sometimes there are differences in usage between different publishers.) Some words can be used either way, with a lowercase or capital letter depending on the meaning.