Sounds like you got bundle hoods which are junk. Each lens generally has its own uniquely-designed hood with a designated number-letter combination that indicates which hood needs to be paired with it for maximum benefit. So for example, if I own an EF-S 18-55mm f3.5-5.6 IS STM lens, I look at this chart, find my lens, and find that it requires the EW-63C petal hood. I wouldn't use it on any other lens, as it'll potentially cause vignette problems like you're seeing.

The hoods also generally attach to the lens using a bayonet mount system, not screw-on. This is to prevent the filter issues that you're experiencing.

You don't necessarily need to buy the Canon-branded ones, especially for less-expensive lenses, but I find that they hold up better than 3rd party ones. Just my personal experience.