That happened to me. Rub the coins with baking soda and soak again, be sure to have at least 2cm of vinegar on top.
I've never been satisfied with any acid, nic a date or whatever nickels, to me after the application of the acid then your coin is no longer an original coin. Obviously some people like them and that's alright, I'm just saying for myself, you will not see any in my collection.
Did you let the vinegar evaporate? As the water evaporates the acidity of the solution increases. Also you reach a point where the copper and nickel ions that have been dissolved and are in solution reach a saturation point. Once more water evaporates out the solution can no longer keep the ions in solution and they redeposit back on the coin. This could give you the ugly brownish color.