Hahaha... natural parent instinct.
But still, there are tricks of the trade that we can do to avoid being "THAT PARENT". Make it a point to follow and root for your son's teammates. Talk to the other parents and make it a point to focus more on their kids than yours. Focus on the parents, too. Find out who they are outside of being a baseball parent. Eventually, this helps put things in perspective and helps you put less of a microscope on every little thing happening with your son on the field. You'll also enjoy yourself a lot more during those times when things aren't going well for your son on the field (which happens a lot based on the nature of the game). Your son will benefit as well, feeling more free to play for himself, play for his own enjoyment and his teammates instead of having any parent concerns swirling around his head. This may sound a bit strange but, in my observation over the years, it is a sign of a much healthier relationship if the player has to ask mom or dad if they were even paying attention when he got that big hit than if he sees mom or dad pacing and chewing their nails, hanging on every pitch he is involved in.
Make it a point to show genuine interest in the non-baseball things going on in your son's life. When he knows that you know 
that baseball is just one of many things that make up who he is as a person, perspective improves. When he knows that you recognize that baseball is important to him but you won't tolerate something like a bad sixty time or a bad call or a bad game ruin attitude or enjoyment of the game, perspective improves.
Your son will have other chances to have his 60 time clocked. Is this one event on this one day something that is REALLY going to keep him from reaching his baseball aspirations? Does he really not have other strong attributes in his game that he showed? Do you really think that those assessing didn't recognize his speed attribute, even if the clock didn't reflect favorably? Most importantly, what example do you want to set in showing your son how to handle this type of setback where it seems he has been wronged in some way? Those buggers are taking in our reactions and learning... all the time.
OK, I rambled quite a bit... got a bit off track, probably. I do get it with an event like that. Point is, it's still a game. Good days, bad days. Don't worry. Be happy.