Question: a bit of background to the question, I'm a junior developer and we have recently been given flexitime which so far is working well as I get to start at 8am and leave at 4:30pm.

Today I arrived at 7:30 (I like to be early so I can have a coffee in the office before I start my work) however no one arrived to open the office until 9am.

So my question is, should I leave at the the normal time (5:30 pm) or when I would usually leave(4:30 pm)?

Answer: 
Today, work till 5:30. Yes it's not your fault that you couldn't start at 8 - but you still need to ensure you're working your contracted hours. 

Make sure today though that you discuss with your boss what happens in future. If the company is offering flexible hours - they need to ensure you can start work when you want to (because that's the whole point).
Just ask your manager.

Don't assume anything and simply ask. Something odd happened today and you want to know how to proceed as well as set up an example for future instances should it happen again. This is the exact situation where the only correct thing to do is ask your manager.

You shouldn't "just do the work" without asking because depending on your company guidelines that could push you into overtime hours or the like, which may or may not be "ok".

You shouldn't assume the opposite either, since you don't want to short-change your workplace work-hours.

Just ask.