In the first pair, this meaning of "after all" might be more clear if you do separate it with commas. This is a very subtle distinction though, and different readers may disagree.
The second sentence is problematic because spending a lot of money is not an absolutely negative thing as "hurt me a lot."
Perhaps if you said "I had to spend a lot" or "I was forced to spend a lot."
I think YaniraTfe's examples of "after all" are too literal, and this isn't really how the phrase is used.
It has two meanings, one is "despite all indications to the contrary": "I didn't miss the plane after all! (Although I was very late, and I was sure I had missed it, the plane was delayed by two hours)". A misuse of that would be to say "I got up an hour late, missed the train to the airport, and there was no chance of me catching the plane, and I missed it after all."
And the other is: "when everything is considered" or as M-W puts it "in view of all the circumstances". I think it is very difficult to come up with a misuse of that, as bibliolept says. Here is an example: "I didn't manage to get everything done today, I'm only human after all". This is similar to "when all is said and done", "when it comes down to it", etc.
I don't use "after all" to mean 'despite everything". I would use it to mean "when everything is considered":
I don't know why you are surprised that I can speak Chinese. I was, after all, born in Hong Kong, and lived there until I was twelve.
Twenty years ago, when John was in the Senate, his son Tom did not show much interest in politics, but now I see that Tom has become very involved in his party's politics and is running for office. It looks like Tom is his father's son after all.
I think it is one of the more common ones. I suspect the most common one is as part of the expression "after all is said and done".
I agree with Mole that it is used to mean "despite indications to the contrary." I do not think it is at all common, though, to use the phrase to mean "despite everything", which is a different concept.