They do, but that is not the problem. The problem is that they usually try to impose a database design based on the class structure of the application, which will be something that you never would design by hand, and not is optimized for taking advantage of the relational model. Now you have a convoluted database structure and queries filling several screens, and becomes hard to reason about. Now it does not help that you can handcraft queries.
In addition, your data is usually longer lived than the class structure of application, so making a database design based on the object structure means that you can't change your class structure, because you have several terabytes of data you want to keep, following its structure.
If you create your database schema straight from your class structure, then you are probably going to have problems, I think that's pretty much a given.
But if you want to query from an ORM to a reasonably normalized database, then with a bit of thought, you can almost certainly dodge many of the traps that an ORM can lead the unwary.
Then don't use bad ORMs. What you are describing is caused by devs with poor understanding using ORMS as a crutch. That same dev would probably make a crappy schema without the ORM.
In addition, your data is usually longer lived than the class structure of application, so making a database design based on the object structure means that you can't change your class structure, because you have several terabytes of data you want to keep, following its structure.