It may sound like a D to foreigners sometimes because Koreans put their tongue a bit closer to the teeth when they make the ㄴ sound.

I don't know why you felt ㄴ is like D. it can't be. It's all ways N sound. 네 is like "nea".

Right, it may sound that way to you, but it's not actually being pronounced that way. Sound changes do occur in other cases though. You can search advanced pronunciation rules or sound changes and find a wiki with examples.