Please note that Lord Vishnu is both Upendra and Mahendra:
Valmiki Ramayana ६-११७-१६ and ६-११७-१७:
सेनानीर्ग्रामणीश्च त्वं त्वं बुद्धि स्त्वं क्षमा दमः || प्रभवश्चाप्ययश्च त्वमुपेन्द्रो मधुसूदनः |
इन्द्रकर्मा महेन्द्रस्त्वं पद्मनाभो रणान्तकृत् || शरण्यं शरणम् च त्वामहुर्दिव्या महर्षयः |
This is the English translation from one source:
You are the leader of the army and the village headman. You are the intellect. You are the endurance and the subduer of the senses. You are the origin and the dissolution of all, Upendra the Divine Dwarf (Vamana) and (the younger brother of Indra) as also the destroyer Madhu, the demon.
You perform action for Indra, the lord of celestials. Mahendra (the Supreme Ruler), the one having a lotus in one's navel and who puts an end to all in battle. The divine sages pronounce you to be fit to afford protection to all and the refuge for all.
Why do the Vedas describe Lord Vishnu as subordinate or helper of Lord Indra in his battles ?
It is even written in above shloka ६-११७-१७ so no contradiction:
You perform action for Indra, the lord of celestials. Here helper word should not be taken as inferior.
Krishna (incarnation of Vishnu) also helped Arjuna (son of Indra) in Mahabharata battle, does that make him inferior to Arjuna? definitely not.
Why, Lord Vishnu is considered as Adityas in the Vedas?
sons of Aditi
If Vishnu is referred as Aditya that means
either a son of Aditi whose name is Vishnu
or Vishnu's incarnation Vamana (took birth as a son of Aditi).
But not the Lord Vishnu from the Trinity gods directly.
Why Lord Vishnu from Trinity can't be Aditya?
Aditi was Daksha's daughter and as I mentioned Adityas means sons of Aditi. But Trinity gods were already there before the birth of Aditi.
If Aditi named his one son after the name of Lord Vishnu then this Vishnu is not same as the Lord Vishnu from Trinity. Or if from context, it is clear that it is referring Vamana incarnation then these is no confusion at all.
And we all know that Vamana incarnation just happened to help Indra because Bali was about to snatch Indra's throne.
Mohini incarnation also helped Devas.
Krishna incarnation too fought for Devas and killed Narkasura. Even though there was some initial conflict and Krishna encouraged people to worship nature (Govardhan) and not Indra. But Indra and Krishna both were good friends.
Indra sent his chariot to Rama incarnation in the battle with Ravana. Even there is one Sarga in Valmiki Ramayana: Indra's boon to Rama
In all incarnation Vishnu and Indra seems to be friend. Which purana says that Indra and Vishnu were or are enemies?
Update: As per Rakesh Joshi's comment
Sarga 117 of Yudhakand of Valmiki Ramayana can help a little on you follow up questions.
Friend doesn't mean they can not be devotee to each other. For instance,
Lord Shi Rama (an incarnation of Lord Vishnu) is a great devotee to Lord Shiva.
Lord Hanuman (11th Rudra, closely related to Lord Shiva) is a great devotee to Lord Shi Rama.
Does that make Shiva inferior to Vishnu or vice versa?