Why is Lord Krishna called Upendra? Any scriptures which mention the reason?
Sandhi Vichheda of Upendra is Upa + Indra. Here the word Upa have many meanings but two meanings "younger brother" and "above" are relevant here.
Upendra = Upa + Indra = Younger brother of Indra
The youngest son of Aditi is Lord Vishnu's incarnation Vamana (Vishnu). As Vamana is younger brother of Indra, he is also known as Upendra. Due to this reason Lord Rama and Lord Krishna are also known as Upendra.
Upendra = Upa + Indra = Indra of Upari (above) Loka (Goloka which is above Indra Loka)
As per Harivamsha Purana - Vishnu Parva - Chapter 19, above earth is Indraloka (swarga/heaven), above this is Brahmaloka and above this is the Goloka. Hence, Golaka is Upari (avobe) loka.
[Indra to Krishna:]
ahaM kilendro devAnAM tvaM gavAmindratAM gataH |
govinda iti lokAstvAM stoShyanti bhuvi shAshvatam ||2-19-45
I am indra of the gods. Let you be the king of cows. From today, the entire people on the face of earth will praise you eternally as govinda.
mamopari yathendrastvaM sthApito gobhirIshvaraH |
upendra iti kR^iShNa tvAM gAsyanti divi devatAH ||2-19-46
kR^iShNa!, cows have installed you, above me, as their god, indra. At heaven, gods will sing praising you as upendra.
I will explain this using a slokam from Sri Vishnu Sahasranamam.
Upendro vamana: pramsur Amogha: suchirrjida:
In the Vamana Avataram, the fifth Avataram of Sriman Narayana, he incarnated as the son of Aditi, the mother of Devendra and the other Devas, so in that case he is the brother of Indra. Though he was technically the younger brother of Indra, he is 'superior' to him as can be seen from the Sandhi Viched of the word.
Upendra can be split into Upa + Indra.
Reason 2 General perception why Vishnu is called Upendra is because He was the brother of Indra.
Indra was the son of Aditi and Kashyapa prajapathi. Also, Vishnu was born as Vamana to the couple. Hence He is called Upa-Indra.
But is that it?
No. The word can also be broken down to Upara-Indra. Which means, above Indra, i.e. greater than Indra. Though Indra is considered the Lord of Devas, the actual lord is the one who created the universe, the living beings the devatas and even Indra. So He is called Upendra.