We just found out that the filter in our Medela breast pump filter has some mold in it. We have pumped and stored about 5 bottles of milk with that filter. Should we throw the milk away?
I would say yes, you should throw the milk away.
Mold is a microscopic organism. By the time it is visible to us, it has actually spread much further.
In the case of a loaf of bread with one end slice that's slightly moldy, it's advised you throw out the entire loaf. See this article.
The reason for this, is that bread is porous, so the mold spreads microscopically through the pores.
Since the filter for the pump has a lot of surface area for the microscopic fungus to adhere to, you don't have any way of telling which parts are actually contaminated. By the same note, you can't tell the extent of the contamination in the milk.
I would also add, that if mold was able to develop in the pump, then other micro organisms may also have developed.
Make sure you sanitize all the removable parts of the pump, and get replacement parts for any you can't. Medela customer service should be able to help you with replacements, hopefully at no cost to you.
I found one online Q & A (which I won't link, because I didn't find it to be reliable), where a user said their pediatrician said not to worry too much because the mold from breast milk is similar to Penicillin mold and shouldn't be harmful. If you hear others say the same, I would contend that this is a very naive view. Yes, the pump is used for breast milk, but it does not mean that the mold is necessarily from the milk. There may even be yeast, rather than mold, involved. Without analyzing all of the contaminated surfaces, you can't be sure what is growing.