How do you come up with new project proposal/ ideas?

Hi all, I would like to preface by apologising that I am not a postdoc, but a recent MSc graduate in the biosciences field. My main reason for asking this question, is because something I observed during my project placement is the ability to generate project ideas to drive the project forward was a differentiating factor between project progresses. Something I struggle with, is how to develop new project ideas/ proposal, as I’ve never formally learnt this, and don’t know how to begin learning this. Most times I read papers, I think the questions I come up with are very basic and leaning more towards questioning the validity of the data (methods they used, controls, stats test, did they manage to falsify the hypothesis/ claim) and not so much questions about further research.

I would like to improve on this aspect, as I am in the midst of preparing for PhD applications and I know some applications require project proposals. I am particularly struggling how to come up with ideas or how to move a work forward, based on reading one lab’s research paper. I would really appreciate if you guys could share some tips + tricks or mental frameworks you have used, which worked for you guys. Especially, if you have found yourself struggling as I am.

Thank you so much! And apologies if it’s a really out of pocket question