I cant seem to get rid of the ripples when making holes in my model. The hole on the right has loop cut and I tried creaes. Both hold have this weird small flap that keep showing up.
Here is the file if you want to look.model with holes
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As stated by @bertmoog this is result of bad topology. I will not elaborate on that as you have enough information in the link in comments, but I will show you how your topology should look like if you want to use Subdivision Surface modifier.
I don't know how much do you know about modeling so I'll be brief, and if you need more info - ask in comments.
I've started with simple Plane with Mirror modifier on X and Y axes, extruded it upwards along your mesh. After that I've Subdivided it once and used Inset on top face. Then with LoopTools addon I've created Circle from vertices created by Inset, extruded it down and filed with Grid Fill, to achieve hard edges I've used Bevel Tool (not modifier).
Keywords marked with Bold should be enough for you to learn about this simple technique.