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For instance, one swith box contains 3 middle-of-the-run 3-way switches, with one pair of travellers coming in for each switch, and one switched leg up to the lights. Instead of isolating the neutral by switch, the apprentice who wired everything simply took all the neutrals in the box and connected them together.
I assume the travellers come in on 3 conductor, and the switched leg and neutral go to the fixture on a 2 conductor. If so, yes they should be "isolated". The neutral on the 2 cond should only connect to the 3 cond, back to the first switch and cicuit source.

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Upon further investigation, I found that all the boxes were wired this way, even the boxes that contained 2 circuits.
This would only be permitted with a multiwire branch circuit. i.e. with a 3 cond home run the neutrals would connect at this point and carry the imbalance back to the neutral bus. Otherwise it would not be allowed --- It would also be a definite hazard to the next electrician who worked on it!

Sounds like you are correct CT...
If I have misinterpreted your post, could you post a circuit diagram of this.

Len