It sounds like it could be a completely normal thing, or that it could potentially be an early indication of something more. To put your mind at ease I think you should see your GP and just discuss it with them.

My brother did a lot of arm flapping as a young child and he was later diagnosed with ADHD, Asperger's Syndrome and a few other aspects of ASDs. He was a lot younger when he was doing the arm flapping though (maybe 4-6 months) so that was at a completely different developmental stage to your child.