How to repair this laminate bubble

It may be possible to repair, but depending on the underlying material, I would take different approaches.

If it's particleboard, your best bet is trying to patch it with veneer. You can find sheets (for bigger patches) online, or banding at most big box stores. The main problems here are matching the current laminate and applying the patch so it isn't obvious. Some tips: Make sure the surface is clean and ready to take the patch, and try to make the patch as "un-square" as possible, so it doesn't stand out. Tracing paper and a lot of patience are required.

If it's plywood, I would refinish the cabinet. If the laminate problem is from heat, it's going to occur again after the patch. You can apply the same veneer patch method to plywood (it's easier), but this will likely be a recurring problem and you might look into a different cabinet finish or a higher quality laminate.

If the walls aren't square, I bet the cabinets aren't square as well. And nothing says your counter top has to be square as well. The best way to hide out of square rooms is to try and match the existing angles. In this case you will need to make the miter cut a little bit off 45, probably 44. A small angle change can make a huge difference when getting to get things to fit. And even then a slight difference in the overhang on the cabinets will not be as noticeable as any means trying to fix the gap between the counter and wall.