Here's a file for you to look at.
The first thing I did was to run rebuild on your arc'd curve. The bottom area was segmented and kindof broken up, and most likely causing the surface breakage.
The other thing to look at was the messy alignment. Like your base curve is slightly lower than the object to flow, so I moved them to be planar? Also, the base curve should be the same length as the flow object, if you want to be controlling the stretch and length of the flow result.
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