OK, I just mentioned it as a sidenote.
One potential conflict may be the issue of human rights.
"Human rights", according to some Klingon in Star Trek VI "even the word is racist". A simple, relatable (and in fiction almost certainly ham-fisted) example would be an alien society that oppresses or outright enslaves some portion of their populace just out of principle
It can apply to phenotype ("skin" is too dark or scaly or whatever), sex or the place they're born/hatched (Australians need a firm hand). I'm not sure that future humans would be fine with this. I'm just assuming for the sake of argument that we'll become more progressive and egalitarian in the future. Maybe we'll become more bigoted and the aliens will be disgusted with that.
Another conflict may be the issue of expansion and terraforming. Maybe we (or the others) will have a revulsion to the colonization of other worlds and the creation/replacement/adaption of biospheres because it prevents independent evolution of intelligent life in the future. That's the abortion debate on a much larger scale.