InnoDB is the default storage engine for MySQL and InnoDB prefers that there is a PRIMARY KEY defined when a table is defined. Having a unique non-nullable primary key can vastly speed up queries and data is stored by the primary key in a B+ Tree structure.
What if a primary key is not defined, InnoDB will use the first unique key defined as NOT NULL. Failing that, InnoDB generates a hidden clustered index named GEN_CLUST_INDEX on a synthetic column that contains a 6-byte automatically increasing number when rows are inserted. This is a key that you can not use for searches (it is hidden from you!) and is not directly benefitting you. And that is probably not what you want.
To find those columns you need to look in the INFORMATION_SCHEMA with a query like this:
SELECT i.TABLE_ID,
…