My 2c worth.
I see Moon conj Saturn. It's a difficult placement, or can be difficult, but it's supposed to be difficult for the Moon person more, and it is her Moon.Moon falling into his 12th house might mean he doesn't understand her emotions and emotional needs. Together with his Saturn it's possible that she seems too irrational emotionally to him which frustrates him yet he has a difficulty realizing it himself. Her 7th house -- all of this comes out in a long term relationship and can be a source of conflict.
Oops DW Moon conj Saturn. Then x2 everything above. And Scorpio, whew, heavy stuff.
Especially since Scorpio Moon is in a symbolical square to Leo Moon, meaning emotional compatibility doesn't come easily.
He has Uranus conj Moon. In Scorpio, too. That might make him secretive and impulsive at the same time, including being prone to unexpected and rash romantic decisions.
Saturn conj his Moon-Uranus is another difficult aspect, especially since her Saturn is in her 8th house. And see how it overlays his freedom-loving 3rd house. I feel like Saturn conj Uranus is very difficult, it feels more restricting than with Mars, because Mars might want to fight for details but not to change the general picture--where Uranus might want to break the ties, to revolutionize the whole "world" of a relationship. Add to this the fact that all that happens in Scorpio, with Mars' force and Pluto's intensity... yeah, difficult.
You describe her a very gentle person, but a Capricorn Sun with Scorpio Venus-Saturn, Sag Jupiter and Leo Moon... obviously you know her and I don't, but I see nothing soft or yielding in her natal chart besides her diplomatic Libra Mars. Though his Venus in Aries must adore her Scorpio Venus and her Fire Moon.
Venus-Saturn square is another difficult aspect.
I think this is where the problem might lie. There are those difficult aspects concerning 7th and 8th, but I don't see many soft, comfortable aspects to balance them out, apart from Moon-Venus which is tangled up with Saturn, and the things are made more difficult by the not very compatible Moons.
Her Venus trine his Mars, but his Venus opp her Mars, and I always found harsh aspects difficult in reverse (i.e. when Venus is the guy. It's not much though, because sexy aspects can be cool when harsh, but considering the overall picture, might be not helping on the relationship level.
There is another interesting thing in both their natal charts. They both have "tough/strong/assertive" overall charts with weak Mars position. It is a curious contradiction and I think in synastry it can either create problems or help balance them out. Their Mars signs are not too compatible, either, so maybe it's not so much about balance.
I know sign compatibility is a basic, primitive and somewhat outdated thing but it so often worked for me... so I tend to bring it up. Moon sign compatibility for emotional stuff and living together, all sorts of closeness, and Mars sign compatibility for sex and action and physical expression of all kinds. And I get suspicious when I see both having a difficult combo in synastry.
The second chart shows up strangely on my screen, that's the composite, right? Uranus riding Dsc in Scorpio--volatile passions, strange and sudden changes in a relationship.
Since it is "his" Uranus and he has natal Uranus aspects, he might be more comfortable with it.
In short:
Saturn problems touching/overlaying relationship houses
control issues
Moons and Marses don't balance out the aforementioned issues
Uranus involved in a one-sided (his) way
12 house involved - hard to understand/realize things
Mars opp Mercury - hard to discuss them, too
They fit each other's general type, though.
Okay, this is my rather simple analysis , but maybe there will be something useful in it. I haven't read other comments yet to keep my version independent.