The wavy comb... it happens. Not a big deal unless it's so out of true that you pinch bees or damage comb removing frames.
The Queen cells: where were they on the frame? With established nucs it's easy to have them swarm; did you purchase the nuc? Cells this time of year are usually the result of swarming. What was the brrod like (how many in what stages)? That can allow you to make an educated guess about swarming vs. supercedure. They probably were defensive because they were temporarily queenless. So it's a good thing you didn't cut out those queen cells! One of them will be your next queen.
The Queen cells: where were they on the frame? With established nucs it's easy to have them swarm; did you purchase the nuc? Cells this time of year are usually the result of swarming. What was the brrod like (how many in what stages)? That can allow you to make an educated guess about swarming vs. supercedure. They probably were defensive because they were temporarily queenless. So it's a good thing you didn't cut out those queen cells! One of them will be your next queen.