In Scorpia Rising, Mrs Jones says at the end that two of the things that alerted her to the fact that it was Blunt, not Scorpia, who arranged for the sniper at Brookland were that the sniper didn't hit Alex, but said "mission accomplished", and secondly that the sniper seemed to deliberately miss. Given that Scorpia's plan was not to kill Alex, and indeed their plan hinged on getting Alex to Cairo, which the sniper attempt proved the catalyst for, why should this indicate that it was not Scorpia who was responsible?
None of the interrogated Scopria members knew about the sniper. Which would be kind of strange if it were an integral part of their plan.
True, but the way Mrs Jones phrases it makes it sound like the assassination attempt should have been successful, which is confusing as nobody wanted Alex dead at that point.
In Stormbreaker, Sayle holds a contest for a kid to try out the new computer. What was the point of this is the whole point of the Stormbreaker was to kill people?
The Stormbreaker at Sayle's base didn't unleash the deadly smallpox gas anyway.
In-Universe with Alex rightfully pointing out that while MI-6 doesn't want to give a kid a gun they're completely fine with sending him to his death.
Alex himself exercises this on occasion, seeming to think that unless he does it with a gun or some other obvious implement of murder, none of the people killed as a result of his actions, occasionally deliberately (see Dr. Grief) and often directly, seem to count as far as he is concerned. This has the rather dubious result of Alex racking up an impressive body count over the course of the series and yet still seeming to think that he's not a killer.
This is in all probability the only thing keeping the kid sane by this point, so you can't really blame the poor sod.
Mrs. Rothman points this out in Scorpia, while trying to convince Alex to work for her organisation.
Russian Roulette reveals that Yassen knew for a long time that John Rider was a British spy. This puts his last words to Alex at the end of Eagle Strike in a new light. By sending Alex to Scorpia, Yassen was trying to turn Alex, the son of the man who in his eyes betrayed him, against the organization who had carried out that betrayal. At the finish of 'Russian Roulette (the Herod Sayle assassination), Yassen tries to give Alex the choice to leave the spy life. However, Alex continues to not be given that choice by MI6, so Yassen with his last words forces the choice.
Also from Russian Roulette: a chapter on Yassen's Scorpia training gives a list of three MI6 gadgets: a metal-eating cream, a poisoned fountain pen, and a battery transmitter. The first two have been seen before, the cream in Stormbreaker and the pen in the film version of Stormbreaker. So what's the battery doing in that list? It's Foreshadowing of its eventual Chekhov's Gun status.