The areas are missing because of a lack of overlap in treed areas. This is covered in the Data Collection guidelines that are agreed to at the time of upload:
Use LOTS of Overlap in Treed or Crop Areas
Trees are hard to render because they are typically almost always in motion and have a lot of fine detail.
Generally, the orthophoto portion of the processing may turn out fine at 65-70% overlap. However, if there are trees included in survey area and you want the 3D components of the processing to turn out well, we recommend using 80-90% overlap in order to make sure we have enough information to represent the trees properly. Bare trees are extremely hard to reconstruct well due to the complexity of the branches and shadows. Extra overlap should be used but even then it can be difficult. Also, avoid windy days when trees are involved.
For the partial outputs these two links have a full explanation:
tl;dr - The areas that were not covered well enough to reconstruct were filled in with the Flat Map system. The output of the system is available in the Flat Map Patch geotiff file.