Yes, it's very common for aftermarket extended warranties to omit things such as emissions control systems, which are probably more likely to be the source of problems than anything else. You may be covered by your manufacturer's extended emissions systems warranty, but in that case you don't need the aftermarket.
Also aftermarket warranties tend to be 'inclusionary', meaning that they only cover items specifically mentioned in the policy, and this can provide a lot of wiggle room to deny claims. What you want is an 'exclusionary' policy, meaning everything is covered except specifically stated exclusions. This type of policy will be more expensive however. Lastly, many/most dealers will not bill an aftermarket warranty company directly (because they don't want to hassle with claim denials), rather you will probably have to pay for repairs in full up front and then try to recover reimbursement on your own.
This is not to say that an extended warranty can never be useful, but buyer beware and make sure you understand exactly what you are really buying.