Brown spots on brassavola flowers and leaves.
 

I am concerned it is Botrytis. But would like second opinion. Also what do I do if it is. Do I but the flower spike and treat plant with antifungal?
The plant has 3 bloomed flower spikes 2 spikes look affected. Also noticed a spot on a leaf.
I have about 3 new spikes about to bloom.

Botrytis causes spots on some orchid flowers. The spores are everywhere in the air. There is nothing you can spray on the plants that will prevent flower spotting. There is no point to cutting off the flower spike. The best you can do is try to avoid cool, humid and stagnant air when plants are in flower.

This particular plant blooms just fine with very low humidity, so you could even bring it someplace with low humidity a few days before buds open. Botrytis wouldn't be as much of a problem.

Leaf spots are likely something else. B. nodosa is highly resistant to leaf spotting, so it may be old mechanical damage from a bump or a scratch.

image attachment
 

sorry I am having a difficult time attaching images of the issue

images again
 

flower spots (again sorry its all separate)

The flower looks like it got bruised, bitten or bumped, not like Botrytis.

The spots on the leaves are common on this plant. I wouldn't worry about them. This plant often gets spots in very strong light. I don't think your plant has been in such strong light, though, otherwise it wouldn't be such a brilliant green.