Lunch breaks do not count as working hours in the UK. Whenever people talk about a 40-hour work week or working 9-to-5, it's typically understood that those 40 hours do not include lunch breaks and that you're actually working a full 8 hours, which means starting at 8:30, leaving at 17:30 or basically any variation thereof for people with flexible hours. The reason no one mentioned this to you is that this practice is so normal that people with work experience don't really think about it.
If this is your first job this is one of those things that you can't be expected to know. Your manager should have explained this, as part of your onboarding as teaching new employees professional norms is part of the deal when you hire people with no experience, but it's understandable that she forgot. All you really need to do is ask your manager
I just realised that I probably misunderstood the hours that I'm expected to work. I took the classic 9-to-5 literally but our lunch break isn't actually included in that, is it? [....this is where she tells you that's indeed not the case...] I feel pretty silly for not realising this sooner but rest assured that I'll get the full 40 hours in from now on. Is it okay if I make up those hours over the coming week(s)?
The key is to make it clear that you feel bad about "messing up" in your first week due to an honest mistake and that you'll be working a regular schedule from now on. Suggesting that you make up the hours helps with assuring your manager that you want to respect professional norms and the nature of the business relationship you have with the company (their money for your time) but it's likely that your manager will simply tell you not to worry about it.
I would not bother HR with this. It's up to your manager to explain what hours she expects of you and whether you should make up the hours you missed.
On the off chance that this isn't actually your first "real" job, you'd still say pretty much the same thing but you'd explain that your previous employer simply handled this differently.