SimCity buildings in holes

@KStamp18 - That is very strange, it looks like buildings that were placed on roads that were lowered with the raise/lower tool. It's hard to say why the buildings would appear on the surface when they rebuild, then sink to the other road after you save and close. 🤔

Instead of just deleting the buildings, I think I would bulldoze the roads & the maglevs where it's happening to see if there are roads beneath that you can't see. The existing roads that I can see are definitely showing like they're bridges, although I can't see any roads underneath them. After you bulldoze the roads you can see, try drawing a cross road as low as possible (draw the road and then press the N key several times to lower it). If there's a road or tunnel buried underneath, it should become visible if you cross it. Press M to raise roads & make bridges; Press N to lower them & make tunnels

Are you using any mods? If you're using any mods (especially if they affect roads/terrain/buildings) remove them and see if it happens without the mods. If you're using mods, you should be playing offline, so try using "Save As" to create a copy of your city and see what happens on the copy first. Depending on how many mods you're using, you risk corrupting your city if you remove them all. 

After making changes, you can also try repairing the game. Exit SimCity > In Origin, right-click the SimCity icon > Choose Repair Game > let the repair fully complete

I hope you can figure this out. Please let us know how it goes - Happy Building!