Welcome to Loaches Online, gassb.
Please could you tell us a little more about the tank, which may help us to figure out what is going on:

What size is the tank?

How long ago was it moved/set up?

If it was an established tank, how long did it take to move it, and did you do anything to help keep the filter bacteria alive?

What are your current water parameters: ammonia, nitrIte, nitrAte, pH and hardness levels?

Can you tell us a bit about your maintenance regime, i.e. how often you clean the tank, filter & substrate, how you do this, how often you perform partial water changes and how much % of the volume (approx) do you change?

Anything new added to the tank before the problems became apparent?

What temperature are you keeping the tank at?

Any other symptoms such as redness where the swellings are or excessively laboured breathing etc?
Any chance of providing a photograph of the affected fish? Clown loaches are not the easiest of fish to keep and are therefore not the ideal choice for beginners. Providing us with as much information possible will help us to help your fish as best we can.
Emma