In a previous post about citation metrics, I criticised Web of Science for under-estimating citations due to (a) only including stuff that's indexed in ISI, and (b) mistakes in their database that cause citations to be lost.
Although I stand by those criticisms - and I am not the first to make them - it is worth pointing out the something can be done about the second one, at least. In another previous post, I mentioned a paper about Bobtail squid that had cited one of my papers on E. hux proteomics. This was not listed as a citation in ISI due to an error in the reference list for that paper. Fortunately, Thomson Reuters Technical Support allows you to report errors and, I can happily report in this case, they will fix them.
If your Google Scholar count for given paper is higher than for Web of Science, it might therefore be having a quick look at the difference and checking the reference list of those missing papers.