Wow, I don't know how you did this, but each tile that looks empty on your tilemap is actually not. They are all set to transparent tiles with different IDs - 19, 20, 50 etc..
And all tiles in the tilemap (even the transparent ones) by default have collision polygons enabled.
So if you tick "Show collision polygons" in layout properties, you will see that pretty much all tiles in your tilemap now have collisions. The top image is how it should be, the bottom image is what it is now:
I would probably revert back to the old version of the project, because erasing all these transparent tiles will take a lot of time. You can also open the project in beta version of C3 - they added tools to disable collisions for a large group of tiles at once. So you can do that.
I would also advise using a smaller tilemap. Its current size is 20000x20000 px, it must be really difficult to work with such a huge map.