Virtually every year when I grow my seedlings, I notice some very small (about 1-2mm) orange beads growing in the compost in some of the pots. Is this harmful and, if so, how do I get rid of it?
Minerals or contaminates in the water are likely being absorbed into the perlite.
Often times if the water has a high iron content it will collect on the perlite and appear as the orange-red color that you are seeing.
You also could have some fungus growing on the soil surface.
Making sure you have some amount of airflow around the seedling area can help curb fungus growth.
I like to run a small fan near the area of my seedling trays for a few hours a day. The air movement helps prevent excess moisture from forming and makes for good strong seedlings.
Remember to use good, sterile, soilless mix for seed starting and clean potting cells. If you reuse pots always wash them in a mild bleach solution prior to planting.