I have a solid mahogany body that I have finished, and have had to sand the finish off twice!!

I have been using a clear waterbase grain filler called Crystalac. It is a gel type substance that you wipe on and trowel or wipe off.
I put on two coats and then fine sanded, wiped on another coat and fine sanded again. As soon as I put the first coat of clear, there are marks showing up that look like scratches.
I sanded everything off, filled again three coats, being very careful to sand only with the grain.
After 2 or 3 clear coats the pits started showing up. Pits that look like unfilled mahogany.
I have now purchased some EM 5000 waterbase clear coat, that can be sprayed. I am going to sand everything off AGAIN!! and start over.
Has anyone else experienced something like this?