We study the consequences of cancellation of cubic Abelian anomalies inF-theory GUT models that utilise hypercharge flux in the presence of additionalU(1) symmetries. We show that a mixed anomaly between the hypercharge and twoU(1) gauge fields is not automatically canceled in local models based on thespectral cover and therefore imposes additional constraints on local models inF-theory that have not been accounted for so far. The constraints imply thatthere are only two possible classes of models in F-theory GUTs which havefields on matter curves in non-complete GUT representations that are notvector-like under all U(1)s: the ones based on a 3+2 and 2+2+1 split. Wecomment on some phenomenological implications of these results for realisingNMSSM-like models from F-theory GUTs.
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