How can I prevent my jams and pickles from catching fungus?
I do not know where I go wrong but I always have to throw these off because of this fungus problem.

Discard any home-canned food with mold on or in the food. It could be dangerous. It is possible for mold growing on the surface to lower the acidity of the food. If the food becomes low enough in acid, botulism-producing bacteria can start to grow and produce toxin. Even if you scrape the mold off the surface, the toxin remains in the food. Molds, too, produce toxin so that you should discard the food.

This all stems from improper sealing of your jars. NEVER try to re-use the caps! Rings may be re-used - NOT THE CAPS! And if you have any tiny chips in the mouth of your jars - same thing. Anytime there is a faulty seal on a jar - air and mold seeps in causing the darkening of your foods and mold to grow.

Note: make sure you measure your sugar properly when making jams/jellies - too little sugar will cause fermentation as well.

Store all canned goods in a cool, dry place - stored too long and stored too warm will cloud it.

Also make sure you are not using wet spoons or butter knives to spread the jam or rather take out the jam from the bottle.

I would like to second this. I have had times when I had to throw off almost more than half-filled bottles because I used a wet spoon to take it out.