Yes. There are some elements that a protein skimmer will pull out. This isn’t necessarily a reason to not use a protein skimmer, however. You may want to turn your skimmer off temporarily if you’re manually dosing to allow the minor elements supplement time to dilute, but honestly, this is probably unnecessary.
Periodic ICP testing can give you better insight into the typical levels in your reef aquarium water, and you can use that insight to adjust as necessary.