Worse, the varnish may not stick properly to those shiny areas.
Some questions:
Are you wet sanding or dry sanding?
By hand or using a power sander?
What grit have you been using?
If you have thoroughly sanded the boat, working your way down from 80 grit to 220 grit or perhaps even 400 grit, the surface should be plenty smooth enough to varnish. Wet sanding from 100 grit down through finer grits helps remove sanding dust. A wash with warm soapy water followed by a clean water rinse will reveal any shiny spots.
If there are only a few, and they are not deep, you can eliminate them by gentle wet sanding with 220 grit, perhaps followed by a fine 3M pad, gently rubbed, wet. Clean each area with water and dry it until the shiny spot is gone. This method will leave small shallow depressions, and after varnishing, a careful eye will spot them. If this will bother you, then you will have to use a block hand sanding method, wet, with 220 grit, to get rid of the spots.
Be sure there are NO pinholes through the epoxy to bare wood. These will eventually leak, even if the varnish initially covers them, and water will get under the epoxy, leading to dark spots of rot.
Hope this helps. Post back. Lots of others here will have helpful advice.