Yes, it is quite normal and acceptable for brand-new, high-quality optics to have marks visible under certain lighting and even some dust inside.
If scratches are seen on the surface of the optics, there is nothing to worry about. These scratches are called sleeks and are left over from the polishing process. Sleeks will cause a small scattering of light and will not be noticed (not even by a CCD camera).
Bright light, especially if it is highly directional, say from a flashlight, may show irregularities in the optics (scratches, smudges, uneven coatings, and bright spots, depending on the angle at which you view the optics) even in a system that tests out perfectly on a multi-million-dollar optical bench. The vast majority of light passing through optics which test out perfectly is successfully transmitted and/or reflected into your eyepiece or camera at the image plane.
The combined effects of the small percentages of light scatter (instead of going through the scope), though real, cannot be used to judge the scope’s optical quality. In addition, as a part of a good optical tube design, much of this scattered light itself is blocked by baffles and absorbed by blacking, further reducing any impact on a scope’s performance.
Bright light will inevitably reveal some tiny particles of dust even in new, gas-purged optics such as waterproof spotting scopes. Light scattered or blocked by these particles will be completely out-of-focus and have an unnoticeably small effect as seen through the eyepiece or in camera images.
Do not condemn a mirror (or optics) simply on the basis of shining a bright light down the tube. As noted optics expert Harold Suiter has stated, "All mirrors fail such a harsh inspection."