Yes, the basketball referee was correct to penalize only the first violation and award a substitute free throw, as the second violation only counts if it happened before the ball hit the rim.
The official is indeed correct in this situation. In basketball, the rules stipulate that on a free-throw attempt, if a player in a marked lane space steps into the lane (violation by B1) prior to the ball being released from the free-thrower's hands, it is considered a lane violation. The violation by A3 for breaking the plane of the 3pt arc, however, only becomes relevant if it occurs before the ball has hit the rim. Since A1's free-throw attempt was missed, meaning the ball had already hit the rim or backboard, A3's violation is disregarded, and the first violation, committed by B1, is the one penalized by awarding A1 a substitute free throw.
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