Yes, that's exactly what everyone who's been testing 13.1 has been saying for the past month.
Like I said, Apple could easily remedy this by making it a toggle that says Prioritize Deep Fusion or something, so that it does COtF unless it's a Deep Fusion shot (and maybe a Deep Fusion indicator so we know when it's disabling COtF) ...
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Remember, Deep Fusion only works in very specific lighting conditions. If it's too bright, it'll do Smart HDR. Too dark, and it'll go into Night Mode. But in between those two, Deep Fusion kicks in.
Basically what I do to test it is to take a picture with COtF disabled, using the 2x optical zoom (since the aperture of that lens is smaller, it's more likely to use Deep Fusion as the sensor is receiving less light than the wide lens) preferably indoors with a room light on. Or outdoors, as long as it's not bright. Take the picture, tap the preview to see it 'glitch' once the Deep Fusion processing is done, then pop into settings, enable COtF and go back to take the same picture again. Zoom in, and you should be able to see the difference.