Assumptions en masse. Our PoI was apparently Kara Stanton (KS) as Harold had three books out and was entering (all we saw were nine asterisks) into the machine when initially talking to a very groggy Carter disentangling herself from the car wreck. Carter identifies Kara as the main culprit of the wreck/Reese's abduction/FBI man killing and on Harold's computer Kara Stanton's picture shows up. So KS can thus be both victim and perpetrator.
We also know that Harold's numbers are the "non-relevant/non-terrorism" numbers and yet Kara's actions can clearly be defined as terrorist-ish in nature aka cyber warfare. So why the 'cross-over'?
A couple of possibilities: 1) the machine "detoured" KS's number to Harold & Co. to give an early alert to "Daddy" about what is brewing in the background as otherwise the government entities in charge would have kept a lid on it . malware infiltration of the centralized US network) and precious time might have been lost when/if Harold had ever learned of it PRIOR to doomsday in five months;
2) as KS's motives for her deeds were essentially PERSONAL, aka revenge for China op betrayal, she was thus correctly 'filed' under the "non-relevant" list;
Might there be yet another possibility around the twisted corner?
Well, do we believe the machine to be cognizant (Root hinted at it)? If so, is it truly "neutral"= machine-like or as one can posits is it capable of making value-based decisions (remember how it "learns behaviour"? If the latter, than a clear threat to Harold Finch (aka 'Daddy') was identified and the missing few seconds/flicker showing the blow-up of the car might also have shown for example how the car door locks engaged, closing KS and Snow in (or some such thing-aka direct machine interference).
Remember when Reese learned from Fusco a little about Harold's background (S1 E14 final scene), the machine opened a box with three response levels (called "course of action" assessment) under the heading of SYSTEM ADMINISTRATOR SECURITY BREACHED and settled on the lowest " monitor" re Reese. Noteworthy is the fact that the machine's other response levels read as: mid-level "subvert" and highest level "mitigate".
If correct, the machine will not interfere in Harold's personal risk choices (phone-bomb), but will SUBVERT and MITIGATE outside threats, if not covered by Admin's "ground rules" (S2E1).