Similarities in plot, characters, theme, etc. aren't bad. Those are all just surface level things.
One of my favourite books when I was younger was Dealing with Dragons. It had a lot in common with fairytales -- but that's why I liked it, it had all the setting and character types from fairytales that I liked, but they had different personalities and acted differently, so it was fun and interesting. And it wasn't like I'd never seen a princess who didn't want to marry a prince before... but I liked this princess's character. Similarity to existing things doesn't make a story unoriginal at all.
If somebody reads your story and thinks, "well, it's a lot like [insert movie here], except it did this one really interesting thing and took it in a different direction," that's not a bad thing? That's a very successful story! It means you've managed to resonate with something that other people like, but also bring something new to it. That's really good!
If you obsess over pulling out all the "unoriginal" ideas on the surface, and vetoing any concept that's been done before, it will actually make it harder for you to find a way to do something new and interesting. Because a lot of times, what makes a story unique is that it comes from your point of view and it focuses on the parts that matter to you and it's built on your values and experience. But if you pull out all the ideas that have been explored in other stories before, you're not going to have many ideas left to build on, and then you can't even get to the parts that are unique about your version.
What's more, a lot of this is going to come with practice. A lot of times you need the practice of telling a story that's a little unoriginal in places.
BUT ALL THAT SAID: You can't control how other people respond to your work. You can't stop someone else from thinking you got an idea from somewhere else, and all you can really do is shrug and smile and say "I guess great minds think alike." But if someone thinks your character looks like a character from a popular anime, that doesn't mean you have to change your character; you can go on making your story. When readers notice similarities to something, a lot of times, that doesn't mean anything.