Violations... big or small, write them all. Let the players sort it out amongst themselves. When you find that the plans are a mess, there's no telling what other mistakes are sitting there. Feel free to send the plans back to the maker. People tend to get wound up ....but as Tommy, the oldest Henderson boy said, "here's the thing about that".... unless they are just stupid, they know.....they know better.
Maybe they're all just stupid.
A few months back, I rejected plans for an apartment building because (a) the dimensions on the structural drawings didn't match the dimensions on the architectural drawings, and (b) the dimensions on the north side of the architectural plans didn't add up to the same number as the dimensions on the south side. The architect and structural engineer made revisions, we received a new submittal, and the numbers still didn't work so we rejected the plans again.
Third submittal still didn't add up. At that point, the developer went whining to the mayor's office, and we had a telephone conference call with the architect, the engineer, the owner, my boss, my boss's boss (the land use director), the director of economic development, the municipal counsel, and me. The architect immediately started complaining that we were holding up the project for no reason and costing him money. I pointed out three strings of dimensions that didn't agree from one side of the building to the other. I told everyone on the call that I didn't feel I should approve drawings that have obvious errors, because if any of the errors result in a field condition that doesn't comply with the code, we would ave no choice other than to make the developer tear it out and rebuild it.
The architect was suddenly very quiet, and a few days later we received a new submittal on which all the numbers added up.
Sadly, although that was the only one (so far) that involved so many people, the scenario is not unusual. It's almost universal. We VERY rarely get drawings we can approve on the first submission.
Back when I worked as an architect we had a saying about contractors: "Nobody has time to do it right the first time, but they all have time to tear it out and do it over." It seems that saying now applies to architects and engineers.