I think nearly all PhD candidates can point to at least one thing in their thesis or research that’s a Problem.
A specific issue, question, idea, result – a thing – that invites reasoned concern. Non-hypothetical, something you can talk about, analyse, offer opinions on, but perhaps something that is still undecided. Is it good or bad? Right or wrong? Perhaps it opposes conventional thinking, or is different to how your examiners might think or approach a topic.
Unlike vague hypothetical worries – resulting from general nerves over the importance of the viva – a Problem can become a focus for concern that can’t simply be defused by general practice and prep. If you have a Problem, you can’t push it away. You have to work with it. Dig deeper, learn more, write notes, discuss it with your supervisor and be ready to discuss it with your examiners.
Remember too that a Problem is not automatically disqualifying. A good thesis does not mean a perfect thesis. A Problem does not mean a fail or even major corrections. After three or more years of research, there may not be the space to remove all problems or Problems from a thesis. You may simply have to say, “This is as far as I could come.”
Also remember, that after three or more years, if you have a Problem in your thesis, then YOU are the person best qualified to understand it. Your work, talent and time created this Problem, but also made you the person most capable to discuss it in the viva.