Could a "phantom" citation in WoS be a problem? I have recently noticed that for one of my papers Web of Science shows that it is cited in a paper from totally unrelated area. This looked strange, so I checked the paper and found out that it does not cite my paper. (One of my coauthors has the same initials and surname as author of some papers cited there, so the problem might have be caused simply by automated script.)

I have contacted them using the form on their website, explained the mistake and asked them to remove the incorrect citation. The reply was along the lines: "Thanks for contacting us. Cited references have been reviewed. Requested cited reference already available in WOS." This reaction suggests that they thought that I am requesting adding a citation rather than removing it. I am not sure whether I should waste my time in trying to contact them with the same issue again.


  Are there some reasons why having some superfluous citation in WoS or similar database could cause problems for me? 


When I think of any situations where numbers of citations of my papers would be needed for some kind of evaluation, the list of citations would be very probably prepared by me and not drawn directly from some indexing service. So I can simply omit the incorrect citations indexed in WoS. And even if there were some situations where somebody uses WoS as a way to evaluate my work, being cited in one paper does not influence the total result too much.
I believe that you have answered yourself in your question:


  And even if there were some situations where somebody uses WoS as a way to evaluate my work, being cited in one paper does not influence the total result too much.


Nobody expects databases to be perfect.  You are expected to do a reasonable job of self-curation, such that you are not, say, doubling your citation count by adding in many papers by other people.  Small percentage errors, however, will change nothing significant in any evaluation of you and your work.