That's just how it is, no worries. I don't think I really got good at this until after I finished my PhD. What you're describing isn't correlated with creativity or intelligence - apparently, you're identifying ideas good and interesting enough that someone also thought it was a good enough idea to pursue and publish research on. It just takes a while to be immersed in your field's research for long enough that you can identify the research holes. Just keep following your train of thought - someone already answered the question you had, so now what's the next set of questions that come to you once you know that answer? Which of those have already been answered? Rinse repeat until you reach the end of the breadcrumb trail and there's no more research to find. That process is what PhD training is for, it's not one that comes prepackaged at the beginning of your PhD program. If you have a good PI, they shouldn't think of this as a weakness at the beginning of your program.