gm techniques – How should I set up and execute air battles in my session to avoid easy encounters?

I’m running the Storm King’s Thunder campaign, and we are at the portion where the PCs get an airship to travel around in. For the most part, they have had fun with the different weapons and enemies they have faced; however, I find that one or two spellcasting PCs have been using spells such as mind sliver and polymorph to defeat more difficult encounters, such as one with a roc and wyvern. I realize it was legal and made fights funnier, but it does get annoying when it’s happening in almost every fight. Are there any suggestions on how to keep them on track without them making every encounter easy?

I thought of giving the monsters immunity to these effects, but it sounds like a lame excuse for me not being prepared.