How did you setup your homepage? Is it a custom layout assigned to a static page that’s then assigned to as a “static frontpage” from Settings > Reading > Frontpage displays?
If so, that’s the problem. Weird things happen with pagination in WordPress when you try to do it from a static page as your frontpage.
- Go to Settings > Reading > Frontpage displays and select “your latest posts”.
- Then, go to Appearance > Theme Options > Content > Homepage and select your custom layout there.