Found two minor issues, one I've seen throughout 0.95a up to RC12, and another I've been seeing since 0.91a:
In 0.95a RC12, immediately after battle, I hit Take All and the initial cargo limit is slightly higher than what it is after I control click to get rid of the excess. For example, I beat a large bounty, did not recover any ships, and my cargo was at 4967/5114. Since I expected it to be inaccurately high, I control clicked on the stack of metals, and the cargo limit dropped down to 4916.
Often when I loot past my capacity, I have to control click twice to get back to capacity, once to get to the initial limit which is higher than actual, and a second time to get to the actual capacity. This is with the Industry 1 Skill that gives up to 50% more capacity for cargo/fuel/people, which I suspect is related. I have had it happen with fuel before but it did not happen this time, and I'm not sure if this ever happened with crew/marines.
For the Mission CR Issue (Dire Straits and The Last Hurrah were great!), refitting ships before playing the mission can result in a couple ships with lower than normal CR. It's usually a 15% or so drop, even when I did a full strip and manually refit everything, but usually affects just 1-2 ships, and I tend to refit every single one. Rarely, a ship will have reduced CR even without refits. I saw this a lot in 0.91a, and I still see it in 0.95a RC12.