Are there any side effects from wearing orthotics?

Yes. Orthotics are primarily for comfort. If they hurt, they are not helping you. Some orthotics prescribed can make a condition worse such as if an orthotic with a high arch is given to a patient with a cavus foot.
No. I tell my patients that it is their job to wear the orthotics, and my job to make them wearable. A properly made orthotic adds stability to the way a person walks and therefore there.Should be no side effects.