Is an unexpected reference letter inherently a black mark? I recently applied for a math postdoc in Europe. I contacted the number of letter-writers requested in the job ad, all of whom agreed and sent in letters for me. I also included the names of these people in my application.
I then found out that someone else I didn't ask, but who knew I was applying for this job (and would have been my next reference if the number of letters requested was higher) sent in a letter on-spec, without informing me in advance. Is that going to hurt my application at all, assuming that the letter is good? I'm worried it will make me look disorganised for omitting a letter-writer name, or similar.
I doubt that it would be treated as a negative thing, but just a failure of communication. I think that in some places, however, unsolicited letters commenting on a person have legal issues.
You may be asked to explain it, of course, and you might want to talk to that letter writer as well so that you understand what happened. Perhaps they misunderstood something, perhaps something you said.
A negative, but unsolicited, letter might be a serious issue some places and I think that some countries in EU make a point of regulating such things. Maybe elsewhere as well.
However, if they ask for three letters and get four, they might be required to discard one of them and you might not know which. But, in this case, you already told them who would be writing, so it is more likely that the unsolicited letter would be dropped. There doesn't seem to be any interpretation that suggests you were dishonest in any way.