Thanks for your reply.

You mean to say that its better to tell that I dropped out because of some reason, rather than not mentioning it right?
Will this be okay from that professor perspective? and will it affect my application?

I have shortlisted few universities and I need recommendation letters. Back then when I quit PhD, supervisor and I were not in good terms. So, I decided not to ask my supervisor for recommendation. So, I asked my undergraduate professors to give me recommendation and they agreed to do so.

The real problem is when I contact a professor for PhD and tell him that I have a research paper (published with my supervisor back then), will he look into author details? If so, will he contact my supervisor and ask him about me? or, will he only contact my undergraduate professors (with whom I did not do any research)?