2 runners on a base

[vcblue]

R1 on 2nd, R2 on 1st, no outs. B3 bunts up 3rd base line. F5 throws to 1st for the out. For some reason R1 starts running late, F3 throws the F6 on 3rd and R1 gets in to a pickle. R2 is already on second and is not moving. Eventually R1 and R2 are on second. The fielder with the ball first tags R1 and the BU calls safe then she tags R2 and he calls out.
My understanding is the first runner to legally occupy the base is entitled to the base. (8-3-E-Effect). I understand that the force was off once B3 was put out at 1st. However, I still believe R1 should have been called out not R2. The only reason this matters is because R1 is fast and R2 is slow.
Did my partner get it right?