I would give it time.
3 GPM is nothing, for a pond that size. If you said 50, well then you might be more concerned.
A new pond that size will fill the bottom up quickly. Remeember the volume in a bottom , per inch, of a pond is nothing compared to the volume once you get half way up. Then it takes a lot more water to fill. Sounds like that is what happened.
Give it time, with some nice rain falls, and see where it is at. Even then, it will drop and need some more to refill back up. Then it will be a matter of occasional rains to get a basis of water loss versus fill-up.
You might survey your property when it does rain and see if there is anyplace you can create a swale to capture more runoff faster, if you should need it later on.
Like Esshup says, hindsight. But can't do much more without costing some money. And it might be money spent but not needed because of patience. Wait and see what happens in the next year. Start your stocking plans while you are waiting. Lining up what you need and when. That will help pass the time.
Patience......
