Should I be worried that I don't have ideas of questions to ask during seminars?
A conference sessions might have 50 people in it (at least in the conferences I go to), and yet there will only be 3 or 4 questions on each talk, even if five people have questions for every 1 that has the guts to put their hand up and ask it that most people don't have questions for most talks. You might also notice that its the same people that ask questions about every talk.
I wouldn't worry about it, especially if you are just a PhD student. One thing I would say is that questions should be asked from a position of ignorance - that is you ask a question because you genuinely don't know the answer and want to. Not because you think you can trip the speaker up, or make yourself look clever, so questions that you think will make you look dumb might be the best questions.