Simple answer : clean your tools ! Whether you use brushes, sponges, powder puffs or your hands, all your tools must be clean before you apply makeup, and cleaning them just after is also better, it's just easier to clean a foundation brush when the foundation hasn't dried on the bristles.
You have to make sure the foundation doesn't cause any "allergic" reaction.
I would add the formula,it's not a cause per se, but if your skin can't breathe under your makeup (you feel it), then i would say it's easier for a bacteria to develop into a pimple, that's something i've experienced on my skin.
The makeup should be removed all night, period. If you forgot one night, it won't kill you, but technically you've out all day long and exposed to pollution, dirt, pollen, all things you don't want to go to bed with, especially with still makeup on.
The type of product depends on your skintype, a milk or a water is good if you have a sensitive or dry skin, a gel is maybe more adapted to an oilier face.
For mineral foundation, heavy eye makeup, HD foundation and waterproof mascara (basically, everything i use, LOL !), i use a combination of oil and water. I use sweet almond oil for my eyes, and a blend of grapeseed and ricebran for my face, along with chamomile water (it has soothing properties). I apply the products on a cotton pad, but you can also massage the oil on your face and wash everything off.
I follow with my antioxidant moisturizer and eyecream.