Words like 「滅入る」and 「翻る」I just cant understand. When I look at the spelling for えいる and がえる, it just doesn't match with what I hear. with えいる I hear "eh-E-ru", but since い extends え (I think it does) shouldn't it be "meeh-ru"? and with がえる I hear "gah-I-ru". but its an え so shouldn't it be "gah-eh-ru". This is all super confusing to me and I'm probably fundamentally wrong somewhere so any help is greatly appreciated. (I'm a beginner)
It's worth noting that while the えい vowel combination in kana can represent a lengthened え sound, it doesn't always - in some words, it simply represents the え sound followed by the い sound. In the case of 滅入る, the kanji suggest that the め and いる are separate morphemes, so a "long e" pronunciation would be unlikely.
For 翻る, the vowel is definitely an え, but I can certainly see how it might sound like an い in rapid speech. The Japanese え in general is a little closer to い than the "bed" vowel of most English dialects is, and in vowel clusters like this the second vowel isn't always pronounced that distinctly.
I don't know where you originally heard these phrases from, but you'd pronounce these as:
滅入る めーいーる meh-ee-roo
翻る ひーるーがーえーる he-roo-gah-eh-roo
It should be fairly straightforward. Perhaps in the quicker pace of daily ordinary speech the sound might slide or be compressed to the listener.