A&M lost that football game because Kyle Allen didn't have the experience necessary to not leave the game in the refs hands and throw up a hail mary into triple coverage. Any experienced QB knows for sure whether there's a flag on a possible offsides before heaving up a ball in a game losing/winning situation like that.
The baseball call is different, especially in college. Every baseball fan goes into a game knowing that the refs aren't going to be perfect. The refs have never been and never will be perfect in this sport and that will never change. Complaining about a close out/safe call is fighting a losing battle.
The football call is different, but it still fell ultimately in Allen's hands to not lose that game on that given play and that's exactly what he did.