The problem explained needs more context, but, based on the protocol mentioned and the question raised, there could be two issues;

1. The cells haven't been lysed well despite their appearance.

2. There might be an issue with the buffer leading to protein precipitation.

Darshan Panchariya I added a few more details.

in addition, bca looks fine almost the same protein I used to get with other protocols I did. Moreover, I ran them on gel and did housekeeping protein b actin which also looks fine. But I am just worried why the pellet keeps coming everytime I would centrifuge before doing a bca even though I clearly and very precisely separate the supernatant first time when I am performing extraction of protein.

If your gel looks fine (which for me it absolutely does), the problem might not be as bad. Probably some of the leftover unlyzed cell debris get caught up in the supernatant you freeze. i would definitely avoid repeating freeze-thaw cycles, especially for -80C storage. this might further promote protein denaturation and precipitation.

I agree with Sofya Novikova freeze thawing is known to denature protein and cause its precipitation and like I mentioned earlier, the issue might be with cell lysis, but as long as it works fine, it shouldn't cause a problem.

If you have SDS in your lysis buffer, that may precipitate. You could run a gel with an aliquot of the supernatants after each centrifugation. If the signal of your house keeping protein remains about the same, then you are OK. And as mentioned by others, freezing and thawing can cause proteins to denature and to precipitate.