I'd say one of the most common is mis-application of materials. It can go both ways, but I think most often for people new to HPR is to over-build.
For example, it is very easy to read over some of the great build threads of big, fast, giant-motor projects and go down the rabbit hole that your first HPR needs to be built with 3 layers of 10oz fiberglass tip to tip, when in reality, most L1 rockets are fine with just cardboard and wood glue.
I definitely overbuilt my L2 cert rocket to insure there would be no construction issues with firing a J500, but other than that I agree with everything you said. It's very easy to get overly conservative at the cost of considerable loss of performance.