The 7 year data set of the Milagro TeV observatory contains 2.2×1011 events of which most are due to hadronic cosmic rays. These data are searched for evidence of intermediate scale structure. Excess emission on angular scales of ∼10° has been found in two localized regions of unknown origin with greater than 12σ significance. Both regions are inconsistent with pure gamma-ray emission with high confidence. One of the regions has a different energy spectrum than the isotropic cosmic-ray flux at a level of 4.6σ, and it is consistent with hard spectrum protons with an exponential cutoff, with the most significant excess at ∼10TeV. Potential causes of these excesses are explored, but no compelling explanations are found.