Plutacratic, Yes, it does seem to be a disease of some kind. If you want to keep it. Spray with a Rose Bush fungicide for black spot. Cut all the diseased leaves off of the plant. Or, I agree with PG, take them back if you still can. Any way keep it away from all other plants you have.

Allowing it to dry well will help if it's an issue with rotting roots, but those spots in the top pic aren't what overwatering or too dry usually looks like. When Pothos gets too dry, entire leaves turn evenly yellow, starting with those nearest the roots. Some of the damage in the 2nd pic could be from rotting roots but impossible to say for sure from a pic. Just in case it is some type of fungus, try to keep the foliage dry when watering. Pothos researchers at FL U say sudden drop in temps can cause spots like that. My (main) plant that didn't get brought inside seems to have suddenly developed these spots too since we've had a few colder nights in the midst of much warmer days. (There are some more interesting cuttings I've gotten in trade recently and I've lost interest in devoting space inside to the ubiquitous one. Curious at this point if it can survive winter here, so put it in the ground a few days ago. Last winters' experiment of whether it can go 4 months without a drink was successful, though my house isn't as dry as most during winter.) Symptoms - Leaves have scattered brown patches, usually located in the center of the leaf. Control - Low temperatures or abrupt change from very high temperatures to moderate temperatures can cause this discoloration, especially if plants are succulent and growing vigorously. Maintain even, warm temperatures. Here is a link that might be useful: Pothos production guide, UFL

I agree with Keriann. Yes, you should really let them dry out. Matter of fact, once my seedlings are as big as yours, I let them dry out pretty much all the way before I water again. You can tell they need watered when you pick up the flat and it feels light as a feather. Then after you water, it's much heavier. Your method of bottom watering is quite unique, I must say. I think that most folks bottom water the way I do, which is to say setting the cells or cups into a tray of water and letting the plant absorb as much as it wants until you see moisture on the surface of the soil (usually takes anywhere from 5-20 min). Now, I can't say for sure what positive or negative effects your method of watering might have, except that it sure sounds like a pain in the hiney to me, and I somehow doubt that the soil is getting properly saturated. You want to simulate mother nature; a soaking rain. Then you want to let the soil dry out. That's how it is in nature. Roots need water yes, because the plant needs water, but then they need to dry out and get oxygen. Damp soil all the time = no oxygen to the roots. Now, I can't say for certain what part of your program is causing your issues, but I would start bottom watering them as described by letting them absorb water sitting in a tray. I think you will find that using this method, you should only have to water every 3-4 days, or less. I would lay off the ferts for a while, and then make sure only to fertilize when the soil is already damp, or you will burn the roots. I just mix the fert with water, then pour into a tray and bottom water as usual. Give this a shot, see if that doesn't help.

Does this hanging pot have a drain hole that is recessed above the bottom of the pot that holds about 1/2" of water at the bottom? My experience with Pothos has been that if they get too dry, the older leaves turn yellow & fall off, BUT hanging pots are often designed to hold that excess water, which can cause rotting roots, and would produce similar results in the foliage.