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When I was taking out my filter pad to put in some freshwater fungus medicine, then I saw tiny orange worm things in the extra water in the filter. I also saw even smaller bug looking things swimming around in the water. There are tons of them! I also have a plastic cup with a snail in it (dont ask why) and the bug things are invading it too! In my tank I have two bala sharks that are sick. Im not sure what they have but it almost looks like their scales are coming off in patches. The sharks are hardly swimming anymore. Could the bugs or worm things be affecting my fish and what are they??

The bugs and worms are not necesarily the cause of the sharks being sick...but might be a symptom.
We often see lots of little micro life in tanks that do not have corydoras cats or other scavengers
and
we see the bugs and worms in tanks that get overfed and don't get enough water changes.

The biggest problem in your case is that tricolor (Bala) sharks
shock out often with a chemistry change...but I think you have to try this...

Fill a good size bucket with the tank water
catch the tricolor sharks and put them in the bucket

stir the gravel in the tank
siphon out 100% of the tank water
replace all the tank water with new tap water
use any brand of dechlorinator (we like Aquatan) according to the directions
put in 2 TEAspoons of salt per 1 gallon of tank water

set up the filter again

let the tank run for say 30 minutes
put the fish back in the tank

cross your fingers