Did the rising water level from the big rainstorm overtop your pond bank/levee?

If so, you need a pond outlet that can handle your biggest rain event, OR a pond outlet than can handle most rain events with an emergency outlet that can assist in handling the biggest rains. Until your pond is fixed in that regard, any catfish you are growing would be at great risk of loss.

If water if infiltrating through your re-filled crevice, then you should still see some evidence of the water down the bank. Is all of your land rain-soaked, so you can't tell where your leak is located?

Finally, yes it is very difficult to impossible to fill a crevice while water is flowing and get it to seal. Adequate compaction is very difficult to achieve in that case. There are even stories on Pond Boss of people that have compacted repairs into place after a dam was cut by water erosion and then the repair later washed out because it was not "tied" very well to the surrounding material.

I suspect this is NOT the news that you want to hear, but you probably will need to drain the pond down, wait for drier conditions, dig out and widen the crevice, and then compact and join the material to the adjacent bank edges.

Hopefully, one of our "dirt" experts will drop into your thread and give some better advice.

Good luck on restoring your catfish pond!