strange end of game appeal

[bniu]

I had a strange situation at the end of my game. Score tied 3-3, runners on 2nd and 3rd, no outs, home team batting bottom of last inning, we're in what I call a "winning run situation." Batter hits a looper to left field, R2 is running full speed to 3rd, R3 hesitates a bit and then runs to home. R3 misses the plate entirely (and never noticed), R2 then crosses the plate. Batter-Runner ends up at 2nd base (but missed touching first base). Defensive coach comes out to appeal the two missed bases anyways as he says it gets him two extra outs in the book. I went ahead and allowed the appeals, called R3 and BR out and R2 scored the winning run instead of R3. Game is still over. I guess allowing that appeal couldn't hurt?