Very poor game management. Umpires should not be calling time while runners are advancing! Even though they shouldn't, the rules still say that the umpires may call time as they please. This is one those cases where having the right to do something doesn't necessarily mean that it is the right thing to do.
Not much more that a coach can do other than ask about it. And, assuming that he's asking civily, he should get some reasonable explanation other than, "Get back in the dugout".
Umpiring a game efficiently requires an umpire to have a handle on three separate things:
1) Rule knowledge. This is fairly obvious to most people. He has to know the rules and how they are applied.
2) Mechanics. Somewhat less obvious to the casual observer. He has to know what position to get into to make calls, keeping the proper angle and distance to see the plays and use the proper signals to call them.
3) Game management. This involves effectively dealing with coaches, resolving conflicts, handling unusual situations and keeping the game moving at a normal pace. Of the three, this is probaly the one least understood by coaches, players and fans. But when a game is poorly managed, things can go downhill pretty quickly!
While we hear many complaints about an umpire incorrectly applying a rule, my observation is that just as many problems- if not more- are caused by umpires with poor mechanics and game management skills. The sad part is that these are problems of their own making that can easily be avoided.
Calling time when you shouldn't falls under the latter two catagories. Stopping runners from advancing when the ball is live is just asking for trouble. When it blows up in your face and you have a full-scale argument on your hands, you'll have no one to blame other than yourself!