Hi Teresa,
My first thought is that the resin stuck to the side of the cup hasnt mixed well enough. Assuming you are scraping the cup at the end of pouring to get all your resin, this is probably why its wavy. I make a point to scrape my cup and stir utensil several times during the mixing process to get a good mix.
The other thing that may be happening is if your resin is starting to cure, but you are still adding it to the mold. It wont go flat, but instead stack in layers or waves.
Luckily, though, it sounds like your resin is curing appropriately. As you found out, you can just sand the waves off.