It may depend on the area you live in. I don't say "I did not get you". "I'm not following you" means that I don't understand what you're saying, particularly from the point of view of understanding the logic of the argument that you are presenting.
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"I am not following you" can be used by the speaker to convey the fact that they might not be following the train of thought, or the story, etc. that another person is talking about. It is a phrase used while the conversation is still taking place.
"I did not get you" can be used after the train of thought, or the story, ends - and the listener wants to convey that they did not understa