cleaning the tank killed them?

Question
I bought two fish almost 3 weeks ago: a pleco and another "feeder" fish, which the pet store said could possibly be a baby comet or koi.  I have a Tetra in-tank air pump filter in a 2-gallon glass tank (I realize now this was too small for the two of them to be happy for long, but they were doing terrific until I cleaned the tank yesterday). After week 1, I changed out 1/2 the water, treating the fresh water according to the back of the water conditioner bottle.  I have changed the filter twice, and because it kept "backing up" with bubbles, had been rinsing the filter out every 1-2 days.  As I mentioned, they were both doing well: eating, swimming around, and showing quite a personality. Yesterday I decided to do a thorough tank cleaning because the water was getting cloudy again and I saw a lot of waste collecting under the pebbles.  I put them in a container filled with water from the tank, cleaned everything out with cold & hot water (NO baking soda, soap, etc.) and conditioned the water before adding it to the tank.  The temperature of the "old" water the fish were in was slightly cooler than the new water in the tank, but I mixed some of it with the old, and after 5 minutes poured them, water & all, into the clean tank.  I tried not to stress them out through it all, but not sure if I succeeded.
The pleco (Alfred) was dead when I woke up this morning, and my poor "feeder" (Sauce) has been hanging in there all day: fins clamped to sides, floating listlessly at the top and now at the bottom- I think he'll be gone by morning, though.  I noticed tonight his scale/fin coloration has changed (i.e. from white & pale orange tailfin to mostly white with deep orange collected at the base of the tail, and dark orange along the dorsal fin) and his fins have become ragged.  Earlier he also had a long string of refuse hanging that he couldn't seem to get all the way out.  I noticed the pleco also had ragged fins (though I did notice this 2-3 days ago). They've never shown aggressiveness, so I assume its something to do with the water?  I'm a college student and didn't have time today to troubleshoot the problem, but skimmed several sites and keep seeing things like "tank cycle" and a whole host of maladies that can occur with freshwater fish.  I hope I've given enough concise information; this is my first posting and first time owning fish in about 7 years.  I was so excited to finally have something alive to take care of away from home, and now I feel I've murdered them! Thanks for your help.

Answer
Hi Samantha,

First things first, both the fish are not compatible with your tank, and each other. Here's why:

-A Common Plecostomus (Hypostomus Plecostomus) will reach an adult size of 24" and requires an aquarium of no less than 75 gallons.

-A Common Goldfish will reach an adult size of 12", and needs an aquarium of 30+ gallons
-A Comet Goldfish will reach an adult size of 24", and needs 50+ gallons or a POND
-A Koi will reach an adult size of 36", and needs a POND

A Goldfish or Koi is a coldwater fish, and needs temperatures of 72F or LESS
A Pleco is a Tropical fish, and needs temperatures of 78F or MORE

The only fish you can keep in a 2-gallon aquarium is a single male Betta. If you want to keep other fish, you will need at least a 10-gallon aquarium. A 10-gallon aquarium is considered the minimum of fishkeeping.

The stress associated with a small tank and the incorrect temperatures plus poor water quality killed them. (In a larger tank, there is enough water volume to help dilute toxins from fish waste).

In fact, 'tank syndrome' is exactly what happened to your fish. Here's the short version:
Fish produce waste, and it decomposes into ammonia. Ammonia is toxic to fish, and there was a build-up of it in the small aquarium.

Right now, I recommend that you change 50% of the water daily (if the fish is still surviving) until you get a larger tank. If the fish is dead, you can purchase a single Betta Fish for your tank. Bettas are extremely hardy, and are an excellent choice for beginners.

It is unlikely there is a problem with your water, since you used a water conditioner. It's just the problem with the tank. (at least you don't have a bowl, the #1 death trap!)

Good Luck, and Happy Fishkeeping!