Why are some subcellular structures not visible using a light microscope?

I hope this helps 
The highest resolution power of a common lab scope is usually 400x. Some may be equipped with an oil immersion lens (1000x) to enhance viewing of other smaller organelles than you saw but are rarely used in regular biology classes. Some organelles require higher magnification so all will not be seen unless you use a transmission electron scope imagery (TES) or even a scanning electron scope...(SEM)good job viewing what you did .Did you stain the samples with iodine or toluidine blue? This could better the contrast to see parts.
there yhu go mami

Digestion because it removes waste