Question: I was recently party to a preliminary hearing in a criminal case in which a 911 call was played. The content of the 911 call was very beneficial to the defendant. During the hearing, the judge said something to the effect of, "It would be a question for the jury whether the caller was 'being honest.'"

In other words, the judge was suggesting that the caller to the 911 was being disengenuous and deliberately conveying a false impression -- something that I think would never occur to most people because the call seemed completely genuine. Also, the caller would have had no motive to faking their mental state. I got the idea that the judge was looking for some angle to discredit the 911 call out of interest to see the defendant convicted.

In any case, from the judge's remark I got the idea that he might say something like that during the trial, or give the jury an instruction designed to make them think the 911 caller was putting on an elaborate act.

Is a judge allowed to do this?

Answer: 
There is a concept of [implicature](https://en.wikipedia.org/wiki/Implicature) that says that meaning is conveyed not only by the meanings of the words, but by the circumstances that are likely to cause someone to utter those words. There is nothing in the literal meanings of the words that says that the witness is lying. Your belief that it conveys that seems to be based on implicature: the judge would not feel compelled to mention it unless they thought the witness is lying.

However, that is not necessarily the case. Certainly if for one witness and one witness only, the judge were to say this without anything else giving them reason to, it could come across as implying that the witness is untrustworthy. On the other hand, if the judge were to say this each time a witness takes the stand, or say it at the very beginning of the trial and indicate that it applies to all witnesses, or say it when prompted by something more than just the witness testifying, such as a party asking the judge to make a decision that they believe relies on an assertion of fact, then this inference is less valid.
Of course he can, but in some jurisdictions he will have to choose his words carefully.

Depending on tone or pace of voice, "it's for the jury to decide (this or that)" will often be heard by the jury to mean "but I don't believe it".

Since the meaning depends on tone or pace of voice, who could ever prove anything against the judge?