In the EU, commercial pork production is almost exclusively done in large-scale indoor operations with hundreds to thousands of animals in one facility. These animals represent hundreds of thousands of Euros worth of investment for their owners and there are stringent laws and regulations in place that require everything that enters these facilities to be effectively sterilized. *Still* we get huge outbreaks of some disease or other every few years that can cripple pork production in entire regions. If pork producers can't keep pathogens out of their operations, just assume no one can do so effectively.
Pigs can contract viruses from humans, which I don't think plants can. Pigs and the horrific conditions they're kept in also creates a perfect breeding ground for bacteria.
Things are a bit cleaner in vertical plant farms as long as they dont use animal biproducts in their process.
Ingress of pathogens into pig farms almost always come through contaminated clothing, tools or fodder, not some fancy human to pig contraction. Vertical/indoor farms will need a lot of human supervision and interaction, as well as water and other inputs from the outside. Making sure that all of this does not lead to contamination (which includes sterilizing the entire facility on a regular basis) is prohibitively expensive in all but the most edgiest of edge cases.
And again: why bother? Market gardens are highly space efficient and can feed hundreds of people from the space normally occupied by a suburban house plot. Locating a market garden outside an agglomeration and transporting the produce an hour or so into the city is also very practical. And of course actual staple crops are shelf stable and can thus be transported anywhere at leisure. This fancy "vertical farming" stuff makes sense on a space station and desert cities flush with petro dollars but that's about it.
I've seen a decent number of agricultural areas where the crops are covered with a vast mesh tent supported by a wood or metal framework. Lets sunlight in, keeps insects out. That seems a lot more economical than building a vertical farm in most countries.
There are edge cases where the technology developed for vertical farms seems very useful: densely-populated, small countries; space stations, and off-world colonies. But for most of Earth? Look at how much of the US is farmland, and then imagine how many expensive towers and associated infrastructure you'd need to replace it.
"PM" (powdery mildew) is a huge problem in indoor grows[1]. It's especially bad in the Marijuana industry where it completely ruins the plants' suitability for sale (potentially lethal if inhaled/smoked), but it affects many other plants as well.
Not the original commenter, but I guess they were referring to the fact that closed (indoor) grow environments universally suffer from fungal (and algal) disease problems.
A lovely example of this is the germination rooms/tanks of malting plants where Barley gets germinated over a few days (2-3) before being dried/kilned to make brewing malt: they all have an on-going battle against fungi and algae, much of which battle takes the form of fungicides/algacides, chlorine washes, strong acids, etc. and they never "win" a permanent victory.
The biggest advantage of indoor farming is that you no longer need to use chemical pesticides and herbicides.