First, I'd like to point out that we weren't vendor the OP was referring to which shipped incorrect parts. We triple check orders to make sure that kind of thing doesn't happen.

When I designed this button style, one of the things I really disliked about what was available, was the sloppy plunger action. So the tolerances are a bit tighter on the EI2 design. Of course, due to the fact that the EI2's, as well as other transparent buttons, are not made from nylon material (they can't be and still do what they do) the surfaces of the material interact a little differently, and do wear a bit.
Also, not all switches have the same thickness (ex. E-Switch= .409", Zippy=.399", etc...) As the material is less flexible, if the area was too tight, the thicker switches would be difficult to install, and may splay the legs enough so that the lighting PCB would not be retained. The thinner ones should never fall out, though, so I'm not sure of the conditions which could be causing this to occur. If there is stress on the wiring, or use of heavy gauge wire with stiff insulation, it could be enough stress to cause the thinner switches to wiggle out when being used. If the leg which holds the switch was bent out a bit when the switch was installed, it could be retaining that shape (see below). Another possibility could be that the lighting PCB isn't seated fully and splaying the switch holder legs just enough to cause the issue.
But there are a few things you can do with the EI2 buttons if the need should ever arise. Just give the parts a good squeeze, and it will retain the shape and tighten the spacing. The material is pretty much unbreakable, so no concerns there. The same can be done with the upper inside of the plunger to loosen the fit a bit, and optionally, a little silicone spray won't hurt anything either if so desired. You shouldn't see any issues after that.
And there is one other very important note: plastics, some more than other, shrink and expand with moisture levels (humidity) and temperature, so it's important to make sure that there is a bit of breathing room around the buttons, and that the nuts aren't tighter than they need to be. This is true for any button. I'm sure it's not the issue in this case, but I have seen folks who have put buttons into holes which were virtually a press fit, and have had similar issues. Just something for new builders to be conscious of, especially when designing a panel to be CNC cut.
As usual, I am always available to help with trouble shooting and to suggest ways to solve issues, so an email to tech support is usually all that's needed to get things working properly if one gets stumped along the way.
*edit*
I just checked out your build photos (very nice, BTW) and I can pretty confidently state that the switch issue is very likely being caused by the wiring used. With wire of that heavy size and type (x2), it's going to be very difficult to retain it in such a way as to relieve the tension on the switches.