Microwave kashrus

If meat was cooked in a microwave in which a stain was found afterwards (not sure if meat or dairy) can the food be eaten

What do you mean by a stain? Was the food you put in the oven covered or uncovered?

there was a slight dried liquid stain and the food was covered with one layer

It’s ok. (try to make sure the microwave is clean in the future.)

Thanks!
Furthermore, I have noticed that some people in my house have not been covering the food they put in the microwave, does this make the Keilim the food was in and other keilim treif? Thanks

Your question is unclear. You are concerned about the kelim, what about the food?

To make it simple, always cover the food you are cooking, with that it makes no difference if the food is dairy, meat, pareve or if you are using a non kosher microwave.

A “stain” is not a problem, but food residue is. So always make sure there is no food stuck to the microwave when you insert your food.

For specific questions we would need specific details to answer.

Hope that helps.

We always assumed that one needed to double wrap food when warming in a non kosher microwave. Are you saying that one layer is sufficient, if you clean the microwave first?

Correct