I have an MES30 digital and haven't noticed this kind of problem. I just got a Thermapro multi probe so I will definitely be eyeballing box temp, etc. in the future.
One thing that can be helpful is making notes. There may not be much of a "recipe" for a smoked butt for instance, but if you keep recipes organized, create one for stuff even like a butt, or ribs, etc. and try to remember to note how many hours and minutes per pound things take to cook. It gives you a solid footing down the road for knowing when to start something and when you can expect stuff to finish based on the size and weight of what the product is. People have been cooking "per pound" for a long time.
Also realize that all recipes are not created equal and until you have repeated stuff yourself you cant be sure. We tend to get a lot of recipes off the web these days and we automatically trust them, but who's to say someone posting a "recipe" for a pork butt smoke wasn't themselves using incorrect temps (telling you 250 but their box was actually at 265 and they may not have even known it...accurately) and typos are a thing too. There could just be bad info.