odd call
 

Bases loaded, one out, fly ball to left, not caught but appeared to be to the runners and BU.
R1 ran home, others stayed, BR stopped at 1st with R3, R2 stayed at 2nd.

Pitcher has ball in circle, R2 now realizes not an out and runs to 3rd;
followed by R3 going to 2nd. Either:
- F1 to F5 beats R2 at 3rd
- F1 to F5 does not beat R2 at 3rd

Who is out and why?

Sounds simple, what am I missing?

First question is ... how long did the pitcher hold the ball, and what was she doing.

If not long, then if R2 beats the throw, she's safe, if not, she's out. R3 is still on the wrong base.

If long (and not making a play), and the pitcher throwing was AFTER R2 left, R2 is out the moment she steps off. and place R3 on 2nd.

As soon as R2 leaves 2B (assuming the pitcher made no play on any runner), the ball is dead. R2 is out. R3 is awarded 2B and the BR is on 1B.

What did BU do in this play? If BU signaled out them there is a correctable mistake situation, advance all base runners, thus bases loaded. If BU did not signal, then I agree with Irishmafia. Keep in mind that the play is still on-going, since there are two runners at first base. The pitcher goes to 3rd for the force out and throwing the ball to 2nd will also be a force out.

What was the pitcher doing?
 

I agree with the others, but I am curious to what the pitcher was doing at the moment R2 left 2nd?

This play sounds like it takes a lot of time to develop. The ball went to the outfield, then back in. I'm curious as to what the coaches were doing?