Why an object may be difficult to see under a properly working microscope?

Question

what is the possible reasons why an object may be difficult to see under a properly working microscope

Answer 1

There are several reasons:  it may be too small for the focusing power of the lens used or it may be clear, so difficult to distinguish from the surrounding medium.

Answer 2

Lots of reasons, depends on the object.  Certain cells, esp. bacteria, are clear, and are easier to see if stained.  Sometimes you need to adjust the light, clean off all the lenses, etc.  Sometimes, if they are alive you get Brownian vibratory motion which makes it hard to distinguish them.  There's probably a thousand reasons.