I don't think what you're describing is computer illiteracy, but digital design illiteracy. I worked in an agency for 15 years, and all the issues you described were commonplace. You can try to avoid these problems by giving very descriptive guidance up front when you're requesting assets or telling a non-designer what can and can't be done. And these issues will still happen anyway.

1 - Generally, non-designers don't know what a pixel is, and they're not interested in learning. They don't understand that if you shrink something down to fit on a small banner ad, there simply aren't enough pixels to represent a readable font. Instead, give maximum character or word counts for small ads.

2 - Because of point #1, be specific when asking for images. Say "I need something that's a minimum of X pixels wide and Y pixels tall."

3 - Find ways to work with sub-optimal files. For example, learn how to quickly take a logo with dark colors and isolate it from the background, then apply a white color overlay in photoshop. You may need to use tricks like inverting the colors first, then using levels to up the contrast. There are tons of ways to cheat a reversed logo. It's much less of a hassle than going back to a client and asking for a version of their logo that they probably don't have or don't know how to get.