What types of hay are you feeding? Any of the grass hays should be ok, but alfalfa is not. About how much hay do they eat a day?
Can you give an exact amount of pellets? Mine get 1/8c per day, each, which is only a very little amount in their little bowl – not even close to half a bowl.
Cut way back on the pellets, but do it slowly. They should not be getting more than 1/4c a day each, assuming they are average 5lb rabbits – if they are bigger or smaller you can adjust from there. I suspect the amount of pellets could be the issue.
I also wonder if they are eating too much while out in the garden. They are probably filling up on a lot of grass and other plants and it’s possible one of those doesn’t agree with them. Even if the plants in the garden aren’t an issue, they could easily be getting too much food if they’re filling up on fresh plants and then getting a large amount of pellets.