1. During the conflict Natasha Kerensky starts giving out weapons to civilians on Falcon worlds to start uprisings. Isn't this against Clan law?
The Blood Spirits provided basic combat training to all their civvies for decades. This wasn’t an issue until the Star Adders “absorbed” (really annihilated) the Spirits during the end stages of the Wars of Reaving. Only when the Spirit civvies took up arms against the Adder warriors did the Adders call foul. Based on that history, I’d say arming your own civvies was left as an internal matter for each Clan to decide unless and until a bigger, tougher Clan decided otherwise.
Arming Spheroid civvies is a bit different. In 3019, Kerlin Ward secretly ordered Wolf’s Dragoons to prepare the Inner Sphere for an eventual Clan invasion. The fact that Kerlin had to do so secretly indicates that such a move would have been viewed as treasonous by other Clan leaders. And that makes sense, as Kerlin was essentially ordering the arming an anticipated enemy, right down to Victor and Hohiro’s Dragoon-built custom Dire Wolf configurations.
That said, no Homeworld Clanners found out about Kerlin’s treason, or he and Clan Wolf would surely have paid the price. The other Clan leaders just assumed that the dirty freebirth Dragoons had gone native.
That’s probably also the case with Nattie K. arming Spheroid civvies during the Refusal War. After the Falcons were all dead or gone from a world, the civvies could have just opened the remaining Falcon weapons depots on their own and proving otherwise would probably be an exercise in frustration.
Treason is treason, but if done in secret or under the fog of war, it’s hard to uncover or prove, even in the real world.
2. Phelan bids mercenaries in his defense of Morges against the Falcons. If the Wolves bid their touman isn't it a violation to add in foreign troops?
It’s disgraceful to exceed your bid in a trial of possession, and your codex will take a hit. But it’s no violation of Clan law or custom to bring in additional forces, and probably especially so in a life-or-death, Clan-wide trial of refusal (really annihilation).
The bigger issue was, again, treason, Phelan and the Warden Wolves were defecting to the enemy and joining with them in war against the Clans. At that point, it really doesn’t matter whether Phelan’s force exceeded Ulric’s original bid of Clan Wolf for his trial of refusal. They were now dezgra or worse and not deserving of zellbrigen in the eyes of the Falcons or Clans at large.
Hope this helps.