The existence of the grass after the Reset Charge goes off doesn't necessarily mean that the entire section wasn't disintegrated. That grass presumable existed before and would exist after the infected section of the timeline is pruned, so it would appear as if it hadn't been affected. The same would go for the other things that appeared to be unaffected.
Yeah, but if it is replaced by... an exact different version of itself, that should still result in no significant change. Certainly, you shouldn't be able to create a divergent timeline by disintegrating stuff only to have it replaced by exact duplicates. A new timeline requires a significant change to have occurred.
The enemy Loki probably has specific vulnerable points in time that are all being disintegrated at once.
Does anyone else notice the inherent illogic in having differing points in the time disintegrated "at once"? I expect this represents a fundamental flaw in their time-travel logic, but okay, we'll have to live it with, because comic books.