Bubbles in tomato based recipes

I used to can with my mom so kinda familiar with the basics but she was always running the show. Now my fiancé and I are trying to get into canning and we canned hot and normal salsa, tomato sauce and ketchup. The ketchup and the hot salsa turned out perfect, no separating no bubbles everything sealed. The normal salsa has a good bit of bubbles in them and they move and rise when you jiggle the jar and has a lot of separation all of the jars are like this. The sauce doesn’t have as many bubbles and they don’t move as much as the salsa but I still have a lot of separation. I know separation doesn’t exactly mean it’s unsafe to eat I probably just needed to cook it longer than I did since I used slicing, paste and cherry tomatoes, just whatever I had in the garden. I’m more concerned with the bubbles since they are going to the top when you shake the jar, none of my moms jars turn out like this when she does it but she also doesn’t use a food processor. She did can tomato juice and it bubbles like this too. Anyone know if this is safe and what causes it?