I made a hole. I filled it with water. It had all water source blocks on the top of the hole. I made a pond. I take a bucket and scoop out a block of water. The hole remains. I expect the hole to turn into a water source block to replace the water I took from that space.
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Have you made sure there is water source blocks on every layer? Water will always flow down if it can, so if there is a non-source block underneath the one you took out, the surface layer cannot refill that spot as all the adjacent source blocks flow “down” into the non-source block.
Water can be maddening with this, especially when terraforming coastlines. If you have the patience, you can try putting kelp at the bottom of your pond below and around the problem spot. Kelp can (at least, on Legacy Console, I haven’t checked since I got switched to Bedrock) change a flowing water block into a source block, but it grows insanely slowly at the moment.
If you want it fixed now, and don’t want to fuss around with kelp, fill the pond with sand, or remove the water with a sponge, and put all the water back, starting with the bottom layer.