Using the same antibody to mark astrocytes, we found markings with commonly known shapes, but we also found markings similar to the image below, both in the same animal and in other animals of different ages. The slides are paraffinized and the sections are 10um long. Antigen retrieval was done with citrate buffer, blocking was done with 5% goat serum and 0.3% PBS TX was used. The primary antibodies used were Vimentin (1:250) and GFAP (1:250), and the secondary antibodies Alexa 488 and 555 (1:2000).
Looks like it is likely a tissue problem. Perhaps this is just autofluorescence, which is likely as both wavelengths are positive in these regions. If you post the pictures of the slide with "good" staining more explanation can probably be given. Also, post the species of the primary and secondary antibodies.
The brightest spots here definitely look like red blood cells to me, which are known to be autofluorescent. Maybe this animal wasn't perfused very well.
Also, the intensity of GFAP staining is not homogeneous across the brain, so if you look at a region in which it's almost absent, you may have only the autofluorescence, as Elliot suggested.
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