Umpire didn't call time, so as it stands it is correct (though thankfully most rulesets are finally making illegal pitches just a ball). Since he has made the call, and his partner has not, his partner is not going to say anything without being consulted by the plate official.
Whether calling time was actually justified is a 'had to be there' call. There is the 'heads up' general call you hear all the time - but then there is the ones which are more urgent and different and feel directed directly onto an area you are on. Anyone who has been to the park gets to know which one is which. Also if a lot of balls HAVE been coming into the field, paying attention to those heads up calls should be more important.
The umpire CAN of course call time and if see a lot of distracted players I will - even if I didn't hear something. Also the pitcher HOLDING onto the ball is unusual - I am going to wonder what happened. If I am not sure I may go to my partner without being asked.
It can also depend on the coach reaction as well. If he comes barreling out screaming he isn't getting anywhere. This isn't hard though most coaches seem to insist on getting it wrong - come out politely, say something along the lines of:
"I saw you called IP because she held the ball. What I saw was that she held the ball because most of the players reacted to the 'headsup' call and stopped because they were concerned they could get hit".
You will likely get two responses to that "I heard that, but in my judgement there was no reason for her to stop" or "I didn't hear that or see the other players stop as well". If the umpire says it was his judgement - well that is the end of the discussion - judgement calls are done deals.
If he didn't hear it or see all the players stop, then he can decide whether or not he should confer with his partner. Which he may or may not though in this circumstance there is probably no reason not to.