It is important to make sure you have enough oil to submerge the bites.
Adding too much batter to the pan at once can cause the temperature of the oil to drop rapidly. The funnel cake bites will take longer to cook and will absorb too much oil in the process. Be sure to monitor the oil to ensure it stays at the right temperature continuously while cooking.
If the oil maintains a temperature of 375°F, the funnel cake bites should cook in less than a minute.
As you are frying up your bites, be sure to pick out any pieces of batter that have fallen off into the oil. They will burn and make the bites taste burnt.