Hi Narayan,
Reading on the forums, my understanding is, it is expected to see weird patterns on narrowband flats, and as long as your lights calibrate fine you should be OK. If you are having troubles calibrating your Ha lights, try creating new master flat with different exposure and new flat darks.
Attached is how my Optolong 3nm SHO master flats looks like (ASI533MM Pro). Only STF applied. I recently purchased them, so haven't had a chance to test the calibration.
One of the reasons I chose Optolong, apart from being on sale making it significantly cheaper than Antlia, was reports that Antlia dismiss calls for suspected faulty filters saying it's all normal, while Optolong have in some cases been replacing suspected faulty filters. As Cuiv the lazy geek has showed in one of his videos, unless you have the equipment to test the filters if they pass the right wavelengths, it's a lottery what you get and almost impossible to prove something is wrong with the filter
Sorry, not much of a help, but if you suspect something is wrong, reach out to the retailer you bought the filter from and have a chat with them. They might be more understanding than Antlia.
PS: If you reach out to CN, please post the link here, should be interesting to see what people there share.
PS2: Found the CN link I read in the past with some similarly weird flats:
https://www.cloudynights.com/topic/6...d-sii-filters/. Seems people suggest this is normal. Some suggest trying shorter exposure, different light source, and ensuring flats are taken with the same gain as the lights. Also, if unmounted, check the filters face the correct direction - clean reflective side to the sky/telescope.