The more formal version is the following:
1. The point is . . .
But at some point, this got shortened:
The Point is being . . .
→ Point being . . .
The short form now has informal and idiomatic usage.
Most likely, the confusion over adding is back in again occurs when people get stuck in an intermediate state between the original version and the shortened form.
So, we end up with this kind of situation:
The Point is being is . . .
→ Point being is . . .
It may be used by some people, but it's not really well formed. At best it's redundant, and at worst it could be considered asyntactic. (I would say ungrammatical, but that becomes a grey area when it's actually in use and understood; prescriptivists would call it ungrammatical.)
So, while 3. might be considered idiomatic in certain contexts, it's probably better to use either 1. or 2. And it's certainly better to stick to 1. in strictly formal writing.