Frequently running low on fuel is harder on the fuel pump, and maybe there's some triggering event if a tank is run too low before the pump has "settled in," but even that doesn't exonerate Polaris. In a properly designed system, running around with only a few gallons may shorten the life of the pump(s), but not drastically so; how many people drive their cars around with a quarter tank and only put a couple gallons in at a time? That'd be a lot, and it doesn't seem to be an issue with most cars. Running the tank down to a couple gallons (or less) is pretty standard stuff, especially on mountain sleds; Poo's product testing team would have been foolish not to take a couple new sleds and run them around on fumes. If it's not a problem once the pump has broken in, then they should either bench run the pumps to break them in, or at least put a warning in the manual not to run the tank low the first few rides, but it'd be too late for some people on that.
Anyway, hard to say what the defect is: could just be a run of bad pumps, in which case fuel levels and warm gas are red herrings. Could also be a design issue, and "don't run low on gas" is not a fix. You can't blame Polaris because they can't get new pumps fast enough, but they've definitely got a problem on their hands, and I hope they're doing everything possible to find the cause and fix it.