Exact same situation here, and yes, there are a few hits missing for my son and other players on the team as well. It should be evident who is keeping score at games (I-PAD/Tablet or old fashioned score book). On my son's team, players in the dugout take turn with the score book - generally the pitchers. Don't assume it's a parent unless you are 100% sure.
Important: A D1 coach who was recruiting my son questioned his Max Preps stats. The coach was curious why his number of at bats were lower than other starting players. My son hit over .330, but was a 4th outfielder underclassman on a team full of seniors. He had half of the at bats of a regular starter. My son did not end up committing to this D1 school, to the chagrin of the recruiting coordinator, partly because of the coach's concern over Max preps - there were other reasons of course, not just the Max Preps AB questions.
If a college head coach was questioning stats from Max Preps (mind you this was only at bats in my son's situation) he obviously had more concerns. Some head coaches who recruited my son simply asked what his batting average was, others were more concerned with watching more video, seeing him live again, or simply talking to his high school/travel coaches.
Bottom line, yes it's nice to have that shiny .412 batting average on Max Preps instead of .380 because some hits were missed, but the bottom line is that when it comes to recruiting, Max Preps usually means very little. I was also concerned about the Max Preps stuff for my son but through the recruiting process, I and more importantly he realized it didn't mean much at all.
Good Luck!