Indeed is not immune from typical complaints of large companies.
In general, I found it difficult to understand department-level decisions. This is likely due to sheer hierarchy of the organization (I never met my initial manager's manager for example). My initial product space was discontinued, and I found myself "moved" to a product space that seemed ill-defined (I should have requested to move to something else through an internal job board rather than hoping my manager would do something about it).
I personally strongly disliked how raises and promotions were awarded to engineers. Although it is the same system across roles at Indeed, it seemed like you needed to be prepared to move mountains in order to get relatively small raises (which lead to promotion), but alternatively could do the bare minimum and "coast" on your current salary for quite awhile (i.e. the difference between "exceeding" and "meeting" expectations).
Indeed has been around for 17 years and there are a lot of legacy systems (IQL for example) that while cutting edge for their time have been superseded by other tools. This amounts to a lot of Indeed-specific tech to learn even for experienced people.