Apparently, "playing it safe" is the way Honda wants it. They frown upon "win or crash" riders.
Since none of us actually know what problems may or may not be real with Hayden's bike, it's hard to say what the issue is. But Pedrosa and Puig, given the choice between the standard RCV and the Evolution version, chose the standard version. Hayden, as the lead development rider, didn't have that choice. It's even been reported that Pedrosa, after riding the Evo, has said that he couldn't believe that Hayden had been so fast on it.
I didn't see Pedrosa anywhere near the front today, either. Neither Repsol bike had been at the front this week. Let's not put it all on the riders.