The minor second dischord fits in with the idea of out of tune harmonics. In Just Intonation, the interval depends on which minor second you mean - because each one is slightly different.
For Just, you have to start from a root note. In a major key, that's the root note of the key. For a minor key, I've read it's taken from the relative major, but I'm not sure why, or if that's correct.
Anyway, in one possible version of Just Intonation, the first semitone interval, or minor second, from the root note (lets say C to C#) is 16/15. Using the same idea as before, tone one is f plus its overtones (2f, 3f, 4f...) and tone two is 16f/15, plus its overtones.
The first time two of those overtones concide is the 16th overtone of tone one, with the 15th overtone of tone two (16f = 15x16f/15), so all the lower overtones don't match. Depending on how high the note is, we might not even be able to hear the overtones that do match.
On the same definition of the intervals in Just Intonation (there are other definitions), the diminished fifth from the root note is 45/32 - so the problem is the same; where overtones do coincide, for the two notes, they're very high, and lots of lower overtones exist that can clash / beat / be noticeably out of tune with each other.
The concordant / less discordant intervals are things like perfect fifths (3/2, so the second and third harmonics of the two notes can line up), perfect fourths (4/3 - so the third and fourth harmonics can line up)... and so on.
I'm going by the list of Just ratios given in the fifth paragraph, on this page:
www.chrysalis-foundation.org/just_intonation.htm (a good explanation of the concept)
In the case of any real world instrument we're used to, or any synthesized one with a rich enough timbre, the discord / dissonance is easy to spot. I'm still wondering if it's clear at all with just two sine waves and no overtones / harmonics, or if discord just arises from the clashing harmonics.... Maybe it depends who you ask, I don't know.