Region3 is being wonky

https://gyazo.com/1ff66c6050247a57a9cbb1f938825e29
The trees and the market all have a hitbox, when they touch the market should turn red however it dosnt.
https://gyazo.com/5f7bcb99fb66a4b0ae08dc8da5282e80 However with a tent/smaller building the same exact system works fine
and heres the script

part.Position + 0.5 * part.Size does not work for all rotations, cause part.Size is a vector that lives in the object space of part.CFrame. part.Position + 0.5 * part.CFrame:VectorToWorldSpace(part.Size) is probably what you were trying to accomplish. You can find more information about this in Object and World Space | Roblox Creator Documentation.

Also, using WorldRoot | Roblox Creator Documentation is probably more logical than the for loop you used.

local foundParts = workspace:FindPartsWithIgnoreList(region, ignoreList, 1)
local makeRed = (foundParts > 0)

looks like its because of rotation, you can fix that in a few lines with this module

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That is correct. My fix is incomplete and only works for 4 (straight) rotations, but you will still need to convert part.Size to a world space vector.