Autofluorescence can be a big problem with tissue samples, especially if formalin fixed.  Try soaking your samples in 0.1% sodium borohydride before processing.

Do not formalin fix; even age-related molecules like lipofuscin can contain LPS and different types of amyloids and/or small fragments of LPS/amyloids and all can be auto-fluorescent; use highly specific antibodies with highly dedicated color signals; if you have a convincing quantitative fluorescent difference between controls and your disease state then it is probably a valid observation.