Did you tell Fidelity in February of last year that this was for "the withdrawal of excess contributions"? For example, did you go to their website and find a form for this and use it?
Evidently, they understood this to be a normal withdrawal. This presents a problem. The first solution might be to contact Fidelity and ask if they will, in effect change this request for a normal withdrawal to a request for a withdrawal for excess contributions. If they did, they will issue a new 1099-SA but this time with a distribution code of '2'. Also, if they are on the ball, they should calculate the interest for you - if for no other reason that you don't have access to all the information necessary to do this completely accurately.
However, I have noticed that HSA custodians tend to be reluctant to fix their "mistakes" or anything from the previous year, their mistake or not.
Yes, the 8889 and 5329 will be handled automatically.
Please let me know what Fidelity says before I present you with multiple choices about this 1099-SA.
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