The bubbles can be a result of 2 different reasons. You could have over whisked your custard and accidentally incorporated too much air into the mixture. To prevent this, gently combine your ingredients and avoid whisking in a quick motion. The flan is overcooked. The key to cooking a perfect flan is cooking it LOW AND SLOW. The bubbles could also result from the steamer being too hot and the custard was boiling. This can result in an overly hard custard that is too eggy. To avoid this, turn the heat down to low and carefully monitor it while it is steaming.