I don't know what equipment you were using, so that would be nice to know - camera lens, flash, etc. It is hard to be very definitive with my comments without knowing what you are using and the settings, etc.
I have often used flash to photograph big birds on my trips to Florida. I mount it off camera, and dial it down quite a bit, as has been suggested here. I also use a Better Beamer as I find that tends to spread the flash out, because, I am really only trying to use it as a subtle fill flash. In fact, for me, if you cannot tell that flash has been used then its use has been successful. I also find that dialing it down and using the Beamer, minimizes any shadows that flash can create.
How much you dial it down will depend on the flash you are using and the distance to the subject, so you may have to experiment a bit. A Better Beamer may not be necessary, but I would certainly recommend some type of a diffuser to make the flash effect as subtle as possible.
WesternGuy