Any idea why prototypes have this problem. Or is it simply because they are mostly built by hand 

Most of the time I'm sure someone checks them out and fries the EROm chips with UV light.

I am no expert, but I think you're on the right track. It's not instant, but prolonged exposure will do that. Given that we're talking about 30 year old carts, it's not difficult to ruin the chips. 

This is why you see exposed chips covered with stickers, often with the name of the game and the date written on them. 

The initial flipped bits would likely corrupt the game data such that it still plays and it's not obvious there's anything wrong. Some people might incorrectly assume that most of the game's glitches are "just because it's an unfinished game."

And, of course, bit rot. EPROMs/CD-Rs weren't meant for permanent storage.

Where the hell have you been, Miles? I tried contacting you multiple times.

You often read that "Prototypes will all be dead in a few years." This is hyperbole. Most NES prototypes are made with EPROMs. EPROMs do not last forever. I think they are rated for 15 years. People who deal with them on a regular basis, however, will tell you that they last much longer. For example there are arcade cabinets running with more than a dozen EPROMs from 3 or 4 decades ago. The process by witch they slowly corrupt is called bit rot. Bit rot will be a problem eventually. That is why preservation is so important to some of us.

I have herd of prototypes with loose solder joints. In a lot of cases that can be repaired by a pro with a soldering iron.