3.5 has some really obnoxious potential exploits.
3.5 has some (inherited) unrealism. The standard 3.x coinweight is 1/50 of a pound avoirdupois (291 2/3 dwt), about 5.8dwt (pennyweights) - a not unreasonable coin, a little over the weight of the 5.2dwt of the US Sacajaweah dollar. A hefty coin by medieval standards. THe D&D fixed 1:10:100 Gold:Silver:Copper is a problem - copper was almost never that high in relation by weight, and silver was usually higher; 1:12:96 or 1:20:160 is much more "historical". (At present, tho... 1dwt of 18Kt gold is $52, 1dwt of 90% silver $1.05, and 1 dwt of 95% copper about $0.01 - copper and silver have both been extracted in much higher rates than the medieval period could, and gold costs so much to extract that it's value relative to silver has climbed; further Silver and Copper's decorative uses are far fewer now.) Platinum wasn't even really known in medieval times... at least not in Europe. (It was known and used in gold alloy in the pre-contact Americas.)
The use of undead to provide base level labor is doable. It's about the limit of their ability. Turn a crank, push a broom. I wouldn't trust them to paint things, tho dipping whole objects into pain and putting them back on a different belt might work.
The use of undead squirrels to provide the labor to build a factory I find generates much incredulousity... They can't think, so they can't do the assembly. They lack useful manipulators. Stupid but free willed undead might be able to, but not skeletons as described. They could certainly be used in a cage wheel to provide motive force.
There are some excellent expansions on the medieval economy... but they are, for the most part, incompatible with D&D. D&D has a coin based economy - the medieval one was primarily a barter economy, tho city dwellers (under 2% of the total population) dealt in copper coins ranging from 1 to 10dwt, and wealthier townsmen in silver coins of 1/2 to 10dwt; Gold coins were rarer until later, and represented concentrated wealth, seldom exceeding 10dwt, and often a 1dwt of gold being a common townsman's monthly or seasonal income.
Of course, that leaves out using transmute Rock to mud for tunneling (and thus mountainside homes), and the use of wood frames to turn it into high quality bricks... Fortunately, in D&D, that's not a low level spell, so it's not going to be too disruptive.
So, in the long run, while they don't break the rules, per se, they break willing suspension of disbelief. Further, fixing the rules for the economy is nearly impossible, because of the inherited problems from the original simplifications Gygax used.