I've never cleared a playfield, but I've done quite a few vehicle paint jobs so I'm thinking contaminants left on the playfield before you applied the clear. That is the one time you really want to use fresh wipe cloths. Some waxes can be a pain to get rid of, so a couple of good cleanings may be needed.
It's likely not a lost cause, give it a few days to harden and wetsand the surface to remove all the fish eyes. Then lay another coat or two of clear. If you really want to go nuts, give that coat a week and wetsand it again with some really fine paper and then polish it with a buffer to a mirror finish.