That's really odd, are you sure you aren't in debug mode? Those question mark tiles around the roof are a Throttlekitty tile I have to use to make the slope solid, or else you can glitch through it. None of the packs have updated. Is anyone else having this issue?

I am in debug mode but I don't know why that'd be an issue

That would be why they're showing up like that then. It's a special kind of tile that acts as an invisible wall. It's needed to make the sloped grass walls work. If you don't want the ??? tiles you have to turn off Debug mode, hope that fixes it :)

If I sledgehammer the tiles will it still look the same or will it ruin the look?

You could make the inside of the bunker one big room for sure. But on the exterior I'd be careful, you're character is likely to get stuck under the slope if you sledgehammer the invisible walls and fall down

Same happened to me, I kept playing but when I re opened the game later the ??? tiles disappeared and were replaced by the ones that are supposed to be there. Not sure if this helps but there you go.