Has the reputation change in any way affected how we earn badges?
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Those badges use vote counts, so I doubt it.
Perhaps you have to wait a little, or perhaps it's a bug related to something else, not the reputation change.
Another thing that comes to mind (but is pure speculation), is that perhaps an old answer of you got deleted, so the process detects that you need to have (for example) 3 badges, and it's counting the one you got from the deleted answer (perhaps to a migrated question).