This happened up to Version 6 when the video layer sat inside a frame with its own fill — a card around the clip — and that frame also held layers above the video, like a headline. The card’s colour was drawn over the clip. Version 7 fixes it: update the plugin (Figma does this when you reopen it) and export again. Nothing in your design needs to change.
Try it on your own frame
Free to try, no account. Or watch the plugin work in the browser first.