OK so Yoda was on Naboo, your right. I remember those scenes now.
It seems like only a few droids have special relationships with humans or aliens. Maybe that's why Yoda doesn't acknowledge R2, or visa versa. Yoda didn't have any use for a droid. They had no relationship.
And OB1 saying "come here my little friend" is him just being polite. He has no reason to lie, well except for the fact that he didn't want to tell Luke what happened to his father.
Lucas gave himself a lot of leeway. If you notice, Yoda never mentions anything about not interacting with R2 or anything. Obi-Wan says he doesn't remember ever OWNING a droid, as stated before, but he doesn't say he wouldn't remember R2. Yoda's scene can be interpreted as playing around OR fighting for real. Plus, Luke can't understand the beeps and stuff, so R2 could be saying something and Luke wouldn't have the foggiest what he's talking about. And you can't even say that the translator on the X-Wing debates that, because if you watch the movie, Luke says "we're going to the dagobah system", he never mentions anything about a Jedi Master or Yoda.