I've worked both with ORMs and without. As a general rule, if the ORM is telling you there is something wrong with your query / tables it is probably right.

The only time I've seen this is my career was a project that was an absolute pile of waste. The "CTO" was self taught, all the tables were far too wide with a ton of null values. The company did very well financially, but the tech was so damn terrible. It was such a liability.