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: 
Unless there was a pre-existing conversation with your boss that you were coming in at 8 and that someone would be there to open the office then I'd say that this time you'll just have to take it on the chin and work till 5:30.

What I would do though is explain to your boss (in a non-confrontational, non-accusatory way) that there was no-one to open the office when you arrived and ask if you need to be letting people know about any plans to arrive "early" to ensure a keyholder opens up, or if the office *won't* be opening pre-9:00 on a day you were planning to come in early that you can at least adjust your plans.

Most likely this is just a blip that is down to the organisation adjusting to the flexitime (you mention it is a recent development).
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.