So, Timeline Variance is a Thing, it has an energy signature and can be traced. And we've seen what the temporal reset charges do - they nuke the entire area, but selectively. One would presume that they do so by only targeting people and objects which have a variance signature.
I think the implication is that the charges blitz everything in a small area, so if a person is in the area when the charge drops their entire timeline gets erased thus causing the anomalies
Based on this article, it sounds like the fact that we're not clear exactly how Reset Charges work is a plot point...I gathered that the charges disintegrate the entire section of the timeline allowing it to heal. Enough simultaneously disintegrated sections could cause a lot of trouble.
It does now seem pretty clear that alt-Loki intends to break the "Sacred Timeline" and bring back a multiverse (apparently by deleting various sections of it and forcing divergences). The question is, to what end?