They are different words. 'Inter' is a Latin prefix meaning 'between' e.g. 'an inter-college rugby match'. 'Inner' is an adjective meaning 'interior' e.g. The sleeping bag has a warm inner layer. It's possible that some speakers, particularly if they have an American accent, may pronounce the prefix 'inter' without the 't' sound. However, it is always written 'inter'. Remember that most words don't actually have 'connected speech' forms. In this case, these are two unrelated words.

I think inner means which is completely inside something, and inter means which is pass through something, i just try it, if you get the correct answer, share with me also friend.