Yup, CR is all over the place, especially in the original Monster Manual.My biggest problem is that the challenge rating doesn't really work. Very often, my players steamroll threats that at their appropriate CR. On rarer occasions they get curb stomped by something that shouldn't have been so challenging.
On top of that, the CR system completely falls apart in one of the scenarios 5E is supposed to handle well: A boss monster with a group of low-level mooks. The whole point of bounded accuracy is to make this kind of encounter possible, but the CR system massively overestimates the contribution of the mooks, making it look far deadlier than it is.