In manufacturing process, one develops a product, then they calculate how many of them have to be sold to break even and/or turn a profit. That might take 2 months or it might take 15 years. Thus, when they've ascertained that the B3350 might take 5 years and, for example, 28,224 units sold, to break even, they're going to leave it on the market for a while. Also if there is nothing else that replaces it, so what choice do you have? JD? Mahindra?
Why does it have problems when other equipment uses the same engine? Application. The other applications are mowing equipment. Tractors tend to sit around and idle a lot because that's what many owners were taught and grew up with, and they get used in low-load situations at lower engine RPM. A mowing machine is just the opposite. It runs at maximum RPM and full load continually and typically only during grass growing (and cutting) season. Completely opposite application and usage of a B3350. The smaller the engine the more dependent it is on RPM, loading, thus HEAT in the exhaust system (DPF) to make it work somewhat properly. Secondly, the way the reformer works, it has a tendency to contaminate the engine lube oil with some fuel. The crankcase oil level rises and some of the contaminated oil is forced into the intake manifold/turbocharger through the closed crankcase ventilation system, where it is combusted, but the problem is that it doesn't burn "normally" and thus will carbon/oil foul the turbo, and in this discussion the DPF, much more quickly. This happens on a LOT Of equipment whether or not it has a turbocharger and is one major reason that the engine's lube oil must be checked and changed frequently. I see it all the time. Tractor comes in for "first service", has 400 hours on it and the original engine oil filter and a lot of times the original air filter (which is completely plugged). Owners then get online, gripe about the cost of a 400 hr service, gripe how badly they were treated by the servicing "stealership", and gripe about how poor the equipment is built. It is not isolated to the Kubota brand either. I also sold JD for many years so I know about those shenanigans too.
It's not JUST those reasons, it's a combination of a bunch of them including the software and hardware that is used on the tractor. Kubota's done as much as they can with it as far as the updates; some folks have issues others don't. Dealer I work for sold about 25 of them and thus far 2 have had problems that I know of, which were updated by the many updates and campaigns and have not been back since. The others I don't know about, either they've sold them, traded them, burned them, or they ain't had no problems. Being a service tech, a lot of times I never know what the history is. I just get put on the butt side of the complaining.