I thought it was faked evidence framing Spock so that Section 31 could apprehend him and use their mind-sifter on him. They knew or at least suspected he'd lost his marbles after mind melding with a Red Angel, a potential threat.
The thing is, both Georgiou and Leland freely admitted to knowing all about the Red Angel already - that is, they had access to the fact that it was in fact a Section 31 -sponsored and indeed -run project for time travel. Instead of a "potential threat", S31 would probably consider the phenomenon a "potential leak" - no less a threat to the organization, but not a mystery by any means.
It's not as if S31 could easily come out and tell Starfleet "don't worry, it's just us", though. After all, it wasn't them - a private citizen was using the suit for her own personal goals. And everybody had seen the Signs. Better pretend it was a cosmic mystery, then.
This theory is very good, but sadly not corroborated by the actual show. At that time, Control didn't knew about Spock.
How so? What excuse would Control have for not knowing? Its business is to know all. And we never get hints that it would have failed to know. As soon as Spock decides he's not mad after all and starts making sense to his doctors, his life suddenly is forfeit, supposedly due to Control immediately learning about this.
So we have to accept that either Control knew from the very beginning about Spock, but didn't act on it other than that one deep-fake and then forgot about Spock.
Didn't act? It apparently sent assassins in his way - only they missed him by a few hours, and had to murder his doctors instead.
After this, the hunt was on. Control sent S31 assets after Spock, and one of them soon managed to intercept his getaway vehicle (only Spock wasn't on it, having outwitted his enemies even in a half-wit state).
But Control didn't have hands. It had to tell lies to its field operatives. And thus folks like Leland performed operations that weren't actually necessary, because they tried to solve mysteries that were no mysteries to their de facto boss. Yet the attempt to "probe for information" was quickly revealed to be but another shot at the assassination: even if Leland was blind to this and acted in good faith, Georgiou already knew/guessed better.
Timo Saloniemi