Well, I have to say that it is not a design flaw, but two problems that cause the same result. Some models do have more room in the shift fork guides than others, so they tend to pop out more easily than others. The ones that do come out easier get the updated shift fork installed in the trans to make a tighter fit, which makes it a lot less likely to happen.
If you really did not pull hard on the shifter when yours popped out, then there was another problem in the shifting mechanism. Even if the cables are not adjusted just right they can pop out easier. This is usualy the cause when going from medium range to reverse. If it pops out on any other shift than that, the shift lever was pulled too hard. There can still be two reasons though when it does pop out. It was either reefed on or the dump valve on the transmission is not working or not adjusted.
I work on them all the time and live and work in very mountainous terrain and the only ones that have had an issue were improper operation or needed a cable adjustment. In my area and in talking to all the other techs across the country at training, 90% of all the issues have been a direct result of shifting too hard or quick, and not letting the pressure release from the system to take the torque off the gears. At rare occasions some had the dump valve not working, so people would get frustrated that it wasnt releasing torque and would pull harder (still caused by pulling too hard). The main reason that the earlier models had more issues is because the dealers and the operators were new to the unit, and didnt know how it would react. After some lessons learned, and the dealers starting to tell people how to shift them correctly, the problems went away, at least they did in my area. We sell on average 100 plus rtv's a year, and havent had a issue since, so I think that we have the problem contained.
I am not downplaying your experience, as things do happen sometimes for different reasons, but in my experience with hundreds of customers and the product, there are only two reasons that an rtv ever pops the shift fork out of the rails, and that is pulling too hard on the lever and cables that are out of adjustment. I will agree though that the new fork is a lot harder to pull out, so much so that a couple have broken the shift fork right off in the transmission at the shift collar they pulled so hard.
But the fork didnt pop out......