I have 1 of my six that likes to lay in the water bowl sometimes too, but not at night just for a short time during the day especially when I add clean water. I don't worry so much as it is a short time and she then usually eats some salad and basks right afterward. But even with the cool side during the day around 80 if I am to pick her up from there she does feel cool and same can be said if she has just been sitting on the cool side of the enclosure even out of the water. Just as an example of why I am going into this if you were to use a temp gun and see the surface is 70F, it will feel quite cool to the touch for us, meaning that it is ok if they want to be cooler sometimes as long as its within a good range.
With that said, I would agree that is would be safest to take it out at night for safety for two reasons. One obviously while sleeping you wouldn't want their body to slide down in the water while sleeping for obvious reasons. Two is that while the water technically should equalize to the cool side temps it will be slower than air to warm up in the morning (opposite at night when lights go off).
My suspicion would be that the water was maintaining the temperature from when the lights were on in the enclosure longer after the lights were turned off than the surrounding air (water would be slower to cool than air at this point) and he was using that to try and retain his heat longer.
If you don't have a ceramic heat emitter I would consider adding a small one. It shouldn't be maintaining daytime temps of course, but just a few degrees warmer at night would be beneficial. I aim to have things a stay a little over 65 just in case there is an extra cool night or something I have a safety buffer.